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	<id>https://proteopedia.org/api.php?action=feedcontributions&amp;feedformat=atom&amp;user=Emily+Bradshaw.</id>
	<title>Proteopedia - User contributions [en]</title>
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	<updated>2026-09-28T05:31:42Z</updated>
	<subtitle>User contributions</subtitle>
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		<id>https://proteopedia.org/index.php?title=Pembrolizumab/Keytruda&amp;diff=3029862</id>
		<title>Pembrolizumab/Keytruda</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Pembrolizumab/Keytruda&amp;diff=3029862"/>
		<updated>2019-04-19T14:48:09Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab Antibody Against PD-1 Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Pembrolizumab&#039;&#039;&#039;, trade name &#039;&#039;&#039;Keytruda&#039;&#039;&#039;, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) that is the variable region of the molecule where binding orccurs, as well as a Fab fragment (PemFab) that constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tys101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific T-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
Melanie Kusakavitch was a contributing author.&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Keytruda&amp;diff=2843151</id>
		<title>Keytruda</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Keytruda&amp;diff=2843151"/>
		<updated>2018-01-15T21:44:44Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: Melanie Kusakavtich was also a major contributor to this project.&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab antibody against programmed cell death-1 receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, trade name Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) that is the variable region of the molecule where binding occurs, as well as a Fab fragment (PemFab) that constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated at Asp297&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced [http://www.nature.com/articles/srep35297/figures/2 interaction between Pembrolizumab and PD-1] gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tyr101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminus of PD-L1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in this include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific T-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
Melanie Kusakavitch also contributed equally to this project, but the computer program is not showing her name due to malfunction.&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688696</id>
		<title>Keytruda</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688696"/>
		<updated>2016-12-06T03:08:20Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab antibody against programmed cell death-1 receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, trade name Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) that is the variable region of the molecule where binding occurs, as well as a Fab fragment (PemFab) that constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated at Asp297&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced [http://www.nature.com/articles/srep35297/figures/2 interaction between Pembrolizumab and PD-1] gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tyr101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminus of PD-L1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in this include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific T-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688661</id>
		<title>Keytruda</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688661"/>
		<updated>2016-12-06T02:19:37Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab antibody against programmed cell death-1 receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, trade name Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) that is the variable region of the molecule where binding orccurs, as well as a Fab fragment (PemFab) that constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated at Asp297&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tyr101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminus of PD-L1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in this include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific T-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688660</id>
		<title>Keytruda</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688660"/>
		<updated>2016-12-06T02:18:50Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab antibody against programmed cell death-1 receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, trade name Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) that is the variable region of the molecule where binding orccurs, as well as a Fab fragment (PemFab) that constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated at Asp297&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tys101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminus of PD-L1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in this include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific T-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688654</id>
		<title>Keytruda</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688654"/>
		<updated>2016-12-06T02:14:34Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab antibody against programmed cell death-1 receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, trade name Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) that is the variable region of the molecule where binding orccurs, as well as a Fab fragment (PemFab) that constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated at Asp297&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tys101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminus of PD-L1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific T-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688639</id>
		<title>Keytruda</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688639"/>
		<updated>2016-12-06T01:48:35Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab antibody against programmed cell death-1 receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, trade name Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) that is the variable region of the molecule where binding orccurs, as well as a Fab fragment (PemFab) that constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated at Asp297&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tys101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminus of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific T-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688627</id>
		<title>Keytruda</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688627"/>
		<updated>2016-12-06T01:39:59Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab antibody against programmed cell death-1 receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, trade name Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) that is the variable region of the molecule where binding orccurs, as well as a Fab fragment (PemFab) that constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tys101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminus of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific T-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688623</id>
		<title>Keytruda</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688623"/>
		<updated>2016-12-06T01:33:51Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab antibody against programmed cell death-1 receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) that is the variable region of the molecule where binding orccurs, as well as a Fab fragment (PemFab) that constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tys101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminus of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific T-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688560</id>
		<title>Keytruda</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688560"/>
		<updated>2016-12-05T23:45:55Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab antibody against programmed cell death-1 receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) that is the variable region of the molecule where binding orccurs, as well as a Fab fragment (PemFab) that constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tys101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific T-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688553</id>
		<title>Keytruda</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688553"/>
		<updated>2016-12-05T23:31:06Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab antibody against programmed cell death-1 receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) that is the variable region of the molecule where binding orccurs, as well as a Fab fragment (PemFab) that constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tys101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific T-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688549</id>
		<title>Keytruda</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688549"/>
		<updated>2016-12-05T23:22:57Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab antibody against PD-1 receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) that is the variable region of the molecule where binding orccurs, as well as a Fab fragment (PemFab) that constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tys101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific T-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688548</id>
		<title>Keytruda</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688548"/>
		<updated>2016-12-05T23:22:30Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab antibody against PD-1 receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) that is the variable region of the molecule where binding orccurs, as well as a Fab fragment (PemFab) that constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tys101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific T-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688547</id>
		<title>Keytruda</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688547"/>
		<updated>2016-12-05T23:20:20Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) that is the variable region of the molecule where binding orccurs, as well as a Fab fragment (PemFab) that constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tys101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific T-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688543</id>
		<title>Keytruda</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Keytruda&amp;diff=2688543"/>
		<updated>2016-12-05T23:17:18Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: New page: ==Pembrolizumab antibody against PD-1 receptor== &amp;lt;StructureSection load=&amp;#039;5dk3&amp;#039; size=&amp;#039;350&amp;#039; side=&amp;#039;right&amp;#039; caption=&amp;#039;Full-Length Crystal Structure of Pembrolizumab (PDB code 5dk3)&amp;#039;&amp;gt; == Stru...&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab antibody against PD-1 receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, trade name Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) that is the variable region of the molecule where binding orccurs, as well as a Fab fragment (PemFab) that constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tys101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific T-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Pembrolizumab/Keytruda&amp;diff=2688540</id>
		<title>Pembrolizumab/Keytruda</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Pembrolizumab/Keytruda&amp;diff=2688540"/>
		<updated>2016-12-05T23:15:49Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab Antibody Against PD-1 Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, trade name Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) that is the variable region of the molecule where binding orccurs, as well as a Fab fragment (PemFab) that constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tys101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific T-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Pembrolizumab/Keytruda&amp;diff=2688536</id>
		<title>Pembrolizumab/Keytruda</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Pembrolizumab/Keytruda&amp;diff=2688536"/>
		<updated>2016-12-05T23:14:28Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab Antibody Against PD-1 Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) that is the variable region of the molecule where binding orccurs, as well as a Fab fragment (PemFab) that constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tys101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific T-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Pembrolizumab/Keytruda&amp;diff=2688530</id>
		<title>Pembrolizumab/Keytruda</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Pembrolizumab/Keytruda&amp;diff=2688530"/>
		<updated>2016-12-05T23:09:20Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) that is the variable region of the molecule where binding orccurs, as well as a Fab fragment (PemFab) that constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tys101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific T-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Pembrolizumab/Keytruda&amp;diff=2688529</id>
		<title>Pembrolizumab/Keytruda</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Pembrolizumab/Keytruda&amp;diff=2688529"/>
		<updated>2016-12-05T23:08:53Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) that is the variable region of the molecule where binding orccurs, as well as a Fab fragment (PemFab) that constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tys101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific T-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Pembrolizumab/Keytruda&amp;diff=2688527</id>
		<title>Pembrolizumab/Keytruda</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Pembrolizumab/Keytruda&amp;diff=2688527"/>
		<updated>2016-12-05T23:06:47Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) that is the variable region of the molecule where binding orccurs, as well as a Fab fragment (PemFab) that constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tys101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific T-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688525</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688525"/>
		<updated>2016-12-05T23:01:29Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) that is the variable region of the molecule where binding orccurs, as well as a Fab fragment (PemFab) that constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tys101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific T-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688522</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688522"/>
		<updated>2016-12-05T22:59:59Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tys101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific T-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688516</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688516"/>
		<updated>2016-12-05T22:54:17Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining region (CDR)-L3, CDR-H1, CDR-H2, CDR-H3 of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tys101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific T-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688513</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688513"/>
		<updated>2016-12-05T22:50:16Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining region (CDR)-L3, CDR-H1, CDR-H2, CDR-H3 of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tys101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific T-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688505</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688505"/>
		<updated>2016-12-05T22:42:53Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining region (CDR)-L3, CDR-H1, CDR-H2, CDR-H3 of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tys101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific T-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688432</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688432"/>
		<updated>2016-12-05T19:29:41Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining region (CDR)-L3, CDR-H1, CDR-H2, CDR-H3 of Pembrolizumab. &amp;lt;scene name=&#039;74/745945/Chain_b_amino_acids/1&#039;&amp;gt;Thr30, Tyr33, Ser54, Tys101, Arg102&amp;lt;/scene&amp;gt; on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific t-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688077</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688077"/>
		<updated>2016-12-02T01:08:45Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining region (CDR)-L3, CDR-H1, CDR-H2, CDR-H3 of Pembrolizumab. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous hydrophilic amino acids that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific t-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688075</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688075"/>
		<updated>2016-12-02T01:01:18Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. A very large solvent-accessible surface area of 1,137Å&amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt; is buried on PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; due to the convoluted interaction. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining region (CDR)-L3, CDR-H1, CDR-H2, CDR-H3 of Pembrolizumab. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous hydrophilic amino acids that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific t-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Pembrolizumab/Keytruda&amp;diff=2688072</id>
		<title>Pembrolizumab/Keytruda</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Pembrolizumab/Keytruda&amp;diff=2688072"/>
		<updated>2016-12-02T00:50:21Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. A very large solvent-accessible surface area of 1,137Å&amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt; is buried on PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; due to the convoluted interaction. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with CRD-L3, CDR-H1, CDR-H2, CDR-H3 of Pembrolizumab. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous hydrophilic amino acids that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific t-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688071</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688071"/>
		<updated>2016-12-02T00:47:42Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])&#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. A very large solvent-accessible surface area of 1,137Å&amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt; is buried on PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; due to the convoluted interaction. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with CRD-L3, CDR-H1, CDR-H2, CDR-H3 of Pembrolizumab. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous hydrophilic amino acids that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific t-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688070</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688070"/>
		<updated>2016-12-02T00:46:26Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code [[5DK3]] &#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. A very large solvent-accessible surface area of 1,137Å&amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt; is buried on PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; due to the convoluted interaction. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with CRD-L3, CDR-H1, CDR-H2, CDR-H3 of Pembrolizumab. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous hydrophilic amino acids that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific t-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688069</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688069"/>
		<updated>2016-12-02T00:42:52Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code: [[5DK3]]) &#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. A very large solvent-accessible surface area of 1,137Å&amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt; is buried on PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; due to the convoluted interaction. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with CRD-L3, CDR-H1, CDR-H2, CDR-H3 of Pembrolizumab. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous hydrophilic amino acids that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific t-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688068</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688068"/>
		<updated>2016-12-02T00:41:52Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code: [[5DK3]]) &#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. A very large solvent-accessible surface area of 1,137Å&amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt; is buried on PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; due to the convoluted interaction. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with CRD-L3, CDR-H1, CDR-H2, CDR-H3 of Pembrolizumab. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous hydrophilic amino acids that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass the immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific t-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688066</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2688066"/>
		<updated>2016-12-02T00:27:57Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code: [[5DK3]]) &#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Mechanism ==&lt;br /&gt;
===Pembrolizumab/PD-1 Interaction===&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
===PemFv/PD-1 Interaction===&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. A very large solvent-accessible surface area of 1,137Å&amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt; is buried on PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; due to the convoluted interaction. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with CRD-L3, CDR-H1, CDR-H2, CDR-H3 of Pembrolizumab. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
===PD-L1/PD-1 Interaction===&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous hydrophilic amino acids that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1ECD &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass the immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific t-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Pembrolizumab/Keytruda&amp;diff=2688065</id>
		<title>Pembrolizumab/Keytruda</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Pembrolizumab/Keytruda&amp;diff=2688065"/>
		<updated>2016-12-02T00:18:30Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: New page: ==Pembrolizumab/Keytruda== &amp;lt;StructureSection load=&amp;#039;5dk3&amp;#039; size=&amp;#039;350&amp;#039; side=&amp;#039;right&amp;#039; caption=&amp;#039;Full-Length Crystal Structure of Pembrolizumab (PDB code: 5DK3) &amp;#039;&amp;gt; Click above on &amp;#039;&amp;#039;&amp;#039;edit this...&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code: [[5DK3]]) &#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Pembrolizumab/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== PemFv/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. A very large solvent-accessible surface area of 1,137Å&amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt; is buried on PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; due to the convoluted interaction. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with CRD-L3, CDR-H1, CDR-H2, CDR-H3 of Pembrolizumab. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
== PD-L1/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous hydrophilic amino acids that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1ECD &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass the immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific t-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687779</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687779"/>
		<updated>2016-11-22T15:47:39Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code: [[5DK3]]) &#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Pembrolizumab/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== PemFv/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. A very large solvent-accessible surface area of 1,137Å&amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt; is buried on PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; due to the convoluted interaction. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with CRD-L3, CDR-H1, CDR-H2, CDR-H3 of Pembrolizumab. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
== PD-L1/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous hydrophilic amino acids that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1ECD &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit T-cell function when bound to PD-1, which is located on the surface of antigen-specific T-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass the immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such as metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits T-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific t-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687778</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687778"/>
		<updated>2016-11-22T15:44:45Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code: [[5DK3]]) &#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Pembrolizumab/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to it’s flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== PemFv/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. A very large solvent-accessible surface area of 1,137Å&amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt; is buried on PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; due to the convoluted interaction. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with CRD-L3, CDR-H1, CDR-H2, CDR-H3 of Pembrolizumab. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
== PD-L1/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction.The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous hydrophilic amino acids that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1ECD &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit t-cell function when bound to PD-1, which is located on the surface of antigen-specific t-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass the immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such at metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits t-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific t-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687777</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687777"/>
		<updated>2016-11-22T15:42:11Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code: [[5DK3]]) &#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible and facing the solvent. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Pembrolizumab/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to it’s flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== PemFv/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. A very large solvent-accessible surface area of 1,137Å&amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt; is buried on PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; due to the convoluted interaction. There are a total of 26 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with CRD-L3, CDR-H1, CDR-H2, CDR-H3 of Pembrolizumab. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
== PD-L1/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues that are involved in forming the complex with the N-terminal half of PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; (PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt;/PD-1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; interaction.The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; is in complex with PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt;. The PD-1&amp;lt;sub&amp;gt;ECD&amp;lt;/sub&amp;gt; residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous hydrophilic amino acids that encircle PD-L1&amp;lt;sub&amp;gt;ECD-N&amp;lt;/sub&amp;gt; form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1ECD &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit t-cell function when bound to PD-1, which is located on the surface of antigen-specific t-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass the immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such at metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits t-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific t-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687776</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687776"/>
		<updated>2016-11-22T15:37:58Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code: [[5DK3]]) &#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible and facing the solvent. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Pembrolizumab/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to it’s flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== PemFv/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1ECD contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. A very large solvent-accessible surface area of 1,137Å2 is buried on PD-1ECD due to the convoluted interaction. There are a total of 26 PD-1ECD residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with CRD-L3, CDR-H1, CDR-H2, CDR-H3 of Pembrolizumab. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
== PD-L1/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1ECD residues that are involved in forming the complex with the N-terminal half of PD-L1ECD (PD-L1ECD-N). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1ECD/PD-L1ECD-N interaction.The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1ECD is in complex with PD-L1ECD-N. The PD-1ECD residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous hydrophilic amino acids that encircle PD-L1ECD-N form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1ECD &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit t-cell function when bound to PD-1, which is located on the surface of antigen-specific t-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass the immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such at metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits t-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific t-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687775</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687775"/>
		<updated>2016-11-22T15:37:40Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code: [[5DK3]]) &#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both &amp;lt;sub&amp;gt;CH/2&amp;lt;/sub&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible and facing the solvent. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Pembrolizumab/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to it’s flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== PemFv/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1ECD contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. A very large solvent-accessible surface area of 1,137Å2 is buried on PD-1ECD due to the convoluted interaction. There are a total of 26 PD-1ECD residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with CRD-L3, CDR-H1, CDR-H2, CDR-H3 of Pembrolizumab. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
== PD-L1/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1ECD residues that are involved in forming the complex with the N-terminal half of PD-L1ECD (PD-L1ECD-N). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1ECD/PD-L1ECD-N interaction.The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1ECD is in complex with PD-L1ECD-N. The PD-1ECD residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous hydrophilic amino acids that encircle PD-L1ECD-N form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1ECD &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit t-cell function when bound to PD-1, which is located on the surface of antigen-specific t-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass the immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such at metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits t-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific t-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687774</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687774"/>
		<updated>2016-11-22T15:37:14Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code: [[5DK3]]) &#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both &amp;lt;sub&amp;gt;CH&amp;lt;/2&amp;gt; domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible and facing the solvent. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Pembrolizumab/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to it’s flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== PemFv/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1ECD contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. A very large solvent-accessible surface area of 1,137Å2 is buried on PD-1ECD due to the convoluted interaction. There are a total of 26 PD-1ECD residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with CRD-L3, CDR-H1, CDR-H2, CDR-H3 of Pembrolizumab. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
== PD-L1/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1ECD residues that are involved in forming the complex with the N-terminal half of PD-L1ECD (PD-L1ECD-N). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1ECD/PD-L1ECD-N interaction.The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1ECD is in complex with PD-L1ECD-N. The PD-1ECD residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous hydrophilic amino acids that encircle PD-L1ECD-N form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1ECD &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit t-cell function when bound to PD-1, which is located on the surface of antigen-specific t-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass the immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such at metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits t-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific t-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687773</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687773"/>
		<updated>2016-11-22T15:36:27Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code: [[5DK3]]) &#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both &amp;lt;sub&amp;gt;&amp;lt;CH/2&amp;gt;  domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible and facing the solvent. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Pembrolizumab/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to it’s flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== PemFv/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1ECD contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. A very large solvent-accessible surface area of 1,137Å2 is buried on PD-1ECD due to the convoluted interaction. There are a total of 26 PD-1ECD residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with CRD-L3, CDR-H1, CDR-H2, CDR-H3 of Pembrolizumab. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
== PD-L1/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1ECD residues that are involved in forming the complex with the N-terminal half of PD-L1ECD (PD-L1ECD-N). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1ECD/PD-L1ECD-N interaction.The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1ECD is in complex with PD-L1ECD-N. The PD-1ECD residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous hydrophilic amino acids that encircle PD-L1ECD-N form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1ECD &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit t-cell function when bound to PD-1, which is located on the surface of antigen-specific t-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass the immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such at metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits t-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific t-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687772</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687772"/>
		<updated>2016-11-22T15:35:46Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code: [[5DK3]]) &#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both &amp;lt;CH&amp;gt;&amp;lt;/2&amp;gt;  domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible and facing the solvent. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Pembrolizumab/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to it’s flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== PemFv/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1ECD contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. A very large solvent-accessible surface area of 1,137Å2 is buried on PD-1ECD due to the convoluted interaction. There are a total of 26 PD-1ECD residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with CRD-L3, CDR-H1, CDR-H2, CDR-H3 of Pembrolizumab. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
== PD-L1/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1ECD residues that are involved in forming the complex with the N-terminal half of PD-L1ECD (PD-L1ECD-N). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1ECD/PD-L1ECD-N interaction.The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1ECD is in complex with PD-L1ECD-N. The PD-1ECD residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous hydrophilic amino acids that encircle PD-L1ECD-N form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1ECD &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit t-cell function when bound to PD-1, which is located on the surface of antigen-specific t-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass the immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such at metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits t-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific t-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687619</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687619"/>
		<updated>2016-11-17T02:13:12Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code: [[5DK3]]) &#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH2 domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible and facing the solvent. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Pembrolizumab/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to it’s flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== PemFv/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1ECD contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. A very large solvent-accessible surface area of 1,137Å2 is buried on PD-1ECD due to the convoluted interaction. There are a total of 26 PD-1ECD residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with CRD-L3, CDR-H1, CDR-H2, CDR-H3 of Pembrolizumab. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
== PD-L1/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses again autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1ECD residues that are involved in forming the complex with the N-terminal half of PD-L1ECD (PD-L1ECD-N). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1ECD/PD-L1ECD-N interaction.The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1ECD is in complex with PD-L1ECD-N. The PD-1ECD residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous hydrophilic amino acids that encircle PD-L1ECD-N form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1ECD &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Disease in Humans - Cancer ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit t-cell function when bound to PD-1, which is located on the surface of antigen-specific t-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass the immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight numerous forms of cancer, such at metastatic melanoma and non-small cell lung cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits t-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific t-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687618</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687618"/>
		<updated>2016-11-17T02:07:50Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab/Keytruda==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code: [[5DK3]]) &#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH2 domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible and facing the solvent. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Pembrolizumab/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to it’s flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== PemFv/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1ECD contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. A very large solvent-accessible surface area of 1,137Å2 is buried on PD-1ECD due to the convoluted interaction. There are a total of 26 PD-1ECD residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with CRD-L3, CDR-H1, CDR-H2, CDR-H3 of Pembrolizumab. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
== PD-L1/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses again autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1ECD residues that are involved in forming the complex with the N-terminal half of PD-L1ECD (PD-L1ECD-N). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1ECD/PD-L1ECD-N interaction.The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1ECD is in complex with PD-L1ECD-N. The PD-1ECD residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous hydrophilic amino acids that encircle PD-L1ECD-N form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1ECD &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Disease in Humans - Melanoma ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as non-self and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit t-cell function when bound to PD-1, which is located on the surface of antigen-specific t-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass the immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight metastatic melanoma, a form of cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits t-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific t-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687616</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687616"/>
		<updated>2016-11-17T01:57:25Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code: [[5DK3]]) &#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the whole molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH2 domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible and facing the solvent. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but can be conquered by introducing a serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Pembrolizumab/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
In order for pembrolizumab to block PD-1, pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to it’s flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== PemFv/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The Fv fragment of pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1ECD contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. A very large solvent-accessible surface area of 1,137Å2 is buried on PD-1ECD due to the convoluted interaction. There are a total of 26 PD-1ECD residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with CRD-L3, CDR-H1, CDR-H2, CDR-H3 of pembrolizumab. It is beleived that the sugar chains of PD-1 have no physical contact with pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interaface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
== PD-L1/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses again autoantigens and helps in peripheral immune tolerance. However, when tumors overexpress PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1ECD residues that are involved in forming the complex with the N-terminal half of PD-L1ECD (PD-L1ECD-N). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1ECD/PD-L1ECD-N interaction.The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1ECD is in complex with PD-L1ECD-N. The PD-1ECD residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous hydrophilic amino acids that encircle PD-L1ECD-N form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1ECD &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Disease in Humans - Melanoma ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as nonself and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit t-cell function when bound to PD-1, which is located on the surface of antigen-specific t-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass the immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight metastatic melanoma, a form of cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits t-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific t-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687615</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687615"/>
		<updated>2016-11-17T01:49:45Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code: [[5DK3]]) &#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH2 domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible and facing the solvent. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but can be conquered by introducing a serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. Pembrolizumab contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the whole molecule. &lt;br /&gt;
&lt;br /&gt;
== Pembrolizumab/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
In order for pembrolizumab to block PD-1, pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to it’s flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== PemFv/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The Fv fragment of pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1ECD contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. A very large solvent-accessible surface area of 1,137Å2 is buried on PD-1ECD due to the convoluted interaction. There are a total of 26 PD-1ECD residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with CRD-L3, CDR-H1, CDR-H2, CDR-H3 of pembrolizumab. It is beleived that the sugar chains of PD-1 have no physical contact with pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interaface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
== PD-L1/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses again autoantigens and helps in peripheral immune tolerance. However, when tumors overexpress PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1ECD residues that are involved in forming the complex with the N-terminal half of PD-L1ECD (PD-L1ECD-N). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1ECD/PD-L1ECD-N interaction.The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1ECD is in complex with PD-L1ECD-N. The PD-1ECD residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous hydrophilic amino acids that encircle PD-L1ECD-N form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1ECD &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Disease in Humans - Melanoma ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as nonself and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit t-cell function when bound to PD-1, which is located on the surface of antigen-specific t-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass the immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight metastatic melanoma, a form of cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits t-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific t-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687614</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687614"/>
		<updated>2016-11-17T01:48:41Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code: [[5DK3]]) &#039;&amp;gt;&lt;br /&gt;
_TOC_&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH2 domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible and facing the solvent. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but can be conquered by introducing a serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. Pembrolizumab contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the whole molecule. &lt;br /&gt;
&lt;br /&gt;
== Pembrolizumab/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
In order for pembrolizumab to block PD-1, pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to it’s flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== PemFv/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The Fv fragment of pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1ECD contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. A very large solvent-accessible surface area of 1,137Å2 is buried on PD-1ECD due to the convoluted interaction. There are a total of 26 PD-1ECD residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with CRD-L3, CDR-H1, CDR-H2, CDR-H3 of pembrolizumab. It is beleived that the sugar chains of PD-1 have no physical contact with pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interaface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
== PD-L1/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses again autoantigens and helps in peripheral immune tolerance. However, when tumors overexpress PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1ECD residues that are involved in forming the complex with the N-terminal half of PD-L1ECD (PD-L1ECD-N). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1ECD/PD-L1ECD-N interaction.The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1ECD is in complex with PD-L1ECD-N. The PD-1ECD residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous hydrophilic amino acids that encircle PD-L1ECD-N form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1ECD &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Disease in Humans - Melanoma ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as nonself and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit t-cell function when bound to PD-1, which is located on the surface of antigen-specific t-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass the immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight metastatic melanoma, a form of cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits t-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific t-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687613</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687613"/>
		<updated>2016-11-17T01:47:27Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code: [[5DK3]])&#039; scene=&#039;&#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH2 domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible and facing the solvent. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but can be conquered by introducing a serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. Pembrolizumab contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the whole molecule. &lt;br /&gt;
&lt;br /&gt;
== Pembrolizumab/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
In order for pembrolizumab to block PD-1, pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to it’s flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== PemFv/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The Fv fragment of pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1ECD contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. A very large solvent-accessible surface area of 1,137Å2 is buried on PD-1ECD due to the convoluted interaction. There are a total of 26 PD-1ECD residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with CRD-L3, CDR-H1, CDR-H2, CDR-H3 of pembrolizumab. It is beleived that the sugar chains of PD-1 have no physical contact with pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interaface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
== PD-L1/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses again autoantigens and helps in peripheral immune tolerance. However, when tumors overexpress PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1ECD residues that are involved in forming the complex with the N-terminal half of PD-L1ECD (PD-L1ECD-N). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1ECD/PD-L1ECD-N interaction.The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1ECD is in complex with PD-L1ECD-N. The PD-1ECD residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous hydrophilic amino acids that encircle PD-L1ECD-N form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1ECD &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Disease in Humans - Melanoma ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as nonself and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit t-cell function when bound to PD-1, which is located on the surface of antigen-specific t-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass the immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight metastatic melanoma, a form of cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits t-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific t-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687562</id>
		<title>Sandbox454</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox454&amp;diff=2687562"/>
		<updated>2016-11-16T23:24:40Z</updated>

		<summary type="html">&lt;p&gt;Emily Bradshaw.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Pembrolizumab==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;5dk3&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Full-Length Crystal Structure of Pembrolizumab (PDB code: 5DK3&#039; scene=&#039;&#039;&amp;gt;&lt;br /&gt;
Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Structure and Function ==&lt;br /&gt;
&lt;br /&gt;
Pembrolizumab, or Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The Fc domain is &amp;lt;scene name=&#039;74/745945/Glycosylation/1&#039;&amp;gt;glycosylated&amp;lt;/scene&amp;gt; at both CH2 domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible and facing the solvent. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but can be conquered by introducing a serine-to-proline mutation at &amp;lt;scene name=&#039;74/745945/Pro228/1&#039;&amp;gt;amino acid 228&amp;lt;/scene&amp;gt;, which prevents Fab-arm exchange and stabilizes the molecule &amp;lt;ref name=&amp;quot;log&amp;quot;&amp;gt;DOI:10.1080/17425255.2016.1216976&amp;lt;/ref&amp;gt;. Pembrolizumab contains an Fv fragment (PemFv) and a Fab fragment (PemFab). The Fv fragment is the variable region of the molecule where binding occurs whereas the Fab fragment constitutes the whole molecule. &lt;br /&gt;
&lt;br /&gt;
== Pembrolizumab/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
In order for pembrolizumab to block PD-1, pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to it’s flat conformation when bound to PD-L1 &amp;lt;ref name=&amp;quot;horita&amp;quot;&amp;gt;DOI:10.1038/srep35297&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== PemFv/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The Fv fragment of pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1ECD contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. A very large solvent-accessible surface area of 1,137Å2 is buried on PD-1ECD due to the convoluted interaction. There are a total of 26 PD-1ECD residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with CRD-L3, CDR-H1, CDR-H2, CDR-H3 of pembrolizumab. It is beleived that the sugar chains of PD-1 have no physical contact with pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interaface &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
== PD-L1/PD-1 Interaction ==&lt;br /&gt;
&lt;br /&gt;
The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses again autoantigens and helps in peripheral immune tolerance. However, when tumors overexpress PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1ECD residues that are involved in forming the complex with the N-terminal half of PD-L1ECD (PD-L1ECD-N). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1ECD/PD-L1ECD-N interaction.The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1ECD is in complex with PD-L1ECD-N. The PD-1ECD residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous hydrophilic amino acids that encircle PD-L1ECD-N form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1ECD &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Disease in Humans - Melanoma ==&lt;br /&gt;
&lt;br /&gt;
T-cells are a major component of the immune response in the human body. They have the ability to recognize cancer-related antigens as nonself and eliminate those cells &amp;lt;ref&amp;gt;doi  10.2147/DDDT.S78036&amp;lt;/ref&amp;gt;. PD-L1 and PD-L2 are ligands expressed by some tumors and inhibit t-cell function when bound to PD-1, which is located on the surface of antigen-specific t-cells &amp;lt;ref&amp;gt;doi 10.1007/s40265-016-0543-x&amp;lt;/ref&amp;gt;. When PD-L1 is ligated to PD-1 an adaptive immune response occurs, and this allows cancer cells to bypass the immune surveillance and grow uncontrollably. Pembrolizumab is an FDA-approved treatment that works as a PD-1 pathway inhibitor to fight metastatic melanoma, a form of cancer. As an inhibitor, Pembrolizumab targets the cell death of PD-1 and blocks the immune checkpoint pathway. Pembrolizumab has a very high affinity to PD-1, allowing it to block the interaction between PD-1 with PD-L1 and PD-L2 very efficiently. It antagonizes the interaction between PD-1 and its known ligands, and re-activates anti-tumor immunity &amp;lt;ref name=&amp;quot;log&amp;quot; /&amp;gt;. The PD-1/PD-L1 interaction inhibits t-lymphocyte proliferation, releases cytokines and cytotoxicity, and exhausts tumor-specific t-cells. The inhibition of this pathway reverses the exhausted t-cell phenotype and normalizes the anti-tumor response. One downside of Pembrolizumab is that it may cause inflammatory side effects &amp;lt;ref name=&amp;quot;horita&amp;quot; /&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Emily Bradshaw.</name></author>
	</entry>
</feed>