Sandbox 34: Difference between revisions

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== Structure ==

Papain is a relatively simple enzyme. It consists of only one chain of 212 residues with three disulfide bonds, illustrated in yellow. The single chain is separated into <scene name='Sandbox_34/Subunitsrandl/1'>two domains</scene>, R in purple, and L in gray, that form a cleft in which the <scene name='Sandbox_34/2subuwithactivesite/1'>active site</scene>, consisting of cysteine-25, histidine-159, and asparagine-175, resides.<ref name="PDBSum" /> Many hydrogen bonds exist throughout the molecule, holding it in its 3D conformation. These stabilizing bonds, represented in white, are present both in the <scene name='Sandbox_34/Pap_with_h-bonding_btwnbckbne/1'>backbone</scene>, and between

Papain is a relatively simple enzyme. It consists of only one chain of 212 residues with three disulfide bonds, illustrated in yellow. The single chain is separated into <scene name='Sandbox_34/Subunitsrandl/1'>two domains</scene>, R in purple, and L in gray, that form a cleft in which the <scene name='Sandbox_34/2subuwithactivesite/2'>active site</scene>, consisting of cysteine-25, histidine-159, and asparagine-175, resides.<ref name="PDBSum" /> Many hydrogen bonds exist throughout the molecule, holding it in its 3D conformation. These stabilizing bonds, represented in white, are present both in the <scene name='Sandbox_34/Pap_with_h-bonding_btwnbckbne/1'>backbone</scene>, and between

<scene name='Sandbox_34/Pap_with_h-bonding_btwnsdchns/2'>residues</scene>. Additionally, the molecule is stabilized by <scene name='Sandbox_34/All_bonding_shenanigans/1'>direct protein-protein contacts</scene> consisting of nine hydrogen-bond connections and three ionic interactions.

<scene name='Sandbox_34/Salt_bridges/2'>Salt bridges</scene> strongly contribute to the stability of the structure. The strongest salt bridge exists between

<scene name='Sandbox_34/Salt_bridges/3'>Salt bridges</scene> strongly contribute to the stability of the structure. The strongest salt bridge exists between

<scene name='Sandbox_34/Arg191asp140intraxn/1'>asparagine-140 and arginine-191</scene>.<ref name="Structure" /> A modified cysteine residue with a sulfhydryl group, <scene name='Sandbox_34/9pap_sulfhydryl_group/1'>cysteine sulfonic acid</scene>, is necessary for the activity of the enzyme.<ref>http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html</ref> In 9PAP, the primary representation of papain used in this article, the sulfhydryl group has been oxidized. Papain contains many <scene name='Sandbox_34/Hydrophobicpolar/1'>hydrophobic and polar regions</scene>. The <scene name='Sandbox_34/Hydrophobic_residues/1'>hydrophobic residues</scene> are illustrated in gray, and the <scene name='Sandbox_34/Polar_residues/1'>polar residues</scene> are illustrated in magenta. It is easy to see that the

<scene name='Sandbox_34/Hydrophobicpolar/2'>hydrophobic and polar residues</scene> segregate themselves such that hydrophobic residues are buried within turns or the interior of the molecule, and that polar regions are towards the exterior of the molecule.

Sandbox 34: Difference between revisions

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 == Structure ==
-Papain is a relatively simple enzyme. It consists of only one chain of 212 residues with three disulfide bonds, illustrated in yellow. The single chain is separated into <scene name='Sandbox_34/Subunitsrandl/1'>two domains</scene>, R in purple, and L in gray, that form a cleft in which the <scene name='Sandbox_34/2subuwithactivesite/1'>active site</scene>, consisting of cysteine-25, histidine-159, and asparagine-175,  resides.<ref name="PDBSum" /> Many hydrogen bonds exist throughout the molecule, holding it in its 3D conformation. These stabilizing bonds, represented in white, are present both in the <scene name='Sandbox_34/Pap_with_h-bonding_btwnbckbne/1'>backbone</scene>, and between
+Papain is a relatively simple enzyme. It consists of only one chain of 212 residues with three disulfide bonds, illustrated in yellow. The single chain is separated into <scene name='Sandbox_34/Subunitsrandl/1'>two domains</scene>, R in purple, and L in gray, that form a cleft in which the <scene name='Sandbox_34/2subuwithactivesite/2'>active site</scene>, consisting of cysteine-25, histidine-159, and asparagine-175,  resides.<ref name="PDBSum" /> Many hydrogen bonds exist throughout the molecule, holding it in its 3D conformation. These stabilizing bonds, represented in white, are present both in the <scene name='Sandbox_34/Pap_with_h-bonding_btwnbckbne/1'>backbone</scene>, and between
 <scene name='Sandbox_34/Pap_with_h-bonding_btwnsdchns/2'>residues</scene>. Additionally, the molecule is stabilized by <scene name='Sandbox_34/All_bonding_shenanigans/1'>direct protein-protein contacts</scene> consisting of nine hydrogen-bond connections and three ionic interactions.
-<scene name='Sandbox_34/Salt_bridges/2'>Salt bridges</scene> strongly contribute to the stability of the structure. The strongest salt bridge exists between
+<scene name='Sandbox_34/Salt_bridges/3'>Salt bridges</scene> strongly contribute to the stability of the structure. The strongest salt bridge exists between
 <scene name='Sandbox_34/Arg191asp140intraxn/1'>asparagine-140 and arginine-191</scene>.<ref name="Structure" /> A modified cysteine residue with a sulfhydryl group, <scene name='Sandbox_34/9pap_sulfhydryl_group/1'>cysteine sulfonic acid</scene>, is necessary for the activity of the enzyme.<ref>http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html</ref> In 9PAP, the primary representation of papain used in this article, the sulfhydryl group has been oxidized.  Papain contains many <scene name='Sandbox_34/Hydrophobicpolar/1'>hydrophobic and polar regions</scene>. The <scene name='Sandbox_34/Hydrophobic_residues/1'>hydrophobic residues</scene> are illustrated in gray, and the <scene name='Sandbox_34/Polar_residues/1'>polar residues</scene> are illustrated in magenta. It is easy to see that the
 <scene name='Sandbox_34/Hydrophobicpolar/2'>hydrophobic and polar residues</scene> segregate themselves such that hydrophobic residues are buried within turns or the interior of the molecule, and that polar regions are towards the exterior of the molecule.