3vb8 - Revision history

OCA at 14:22, 14 March 2024

2024-03-14T14:22:39Z

← Older revision		Revision as of 14:22, 14 March 2024
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	<StructureSection load='3vb8' size='340' side='right'caption='[[3vb8]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='3vb8' size='340' side='right'caption='[[3vb8]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3vb8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Synthetic_construct_sequences~~ Synthetic construct ~~sequences~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VB8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VB8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3vb8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VB8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VB8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.9Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vb8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vb8 OCA], [https://pdbe.org/3vb8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vb8 RCSB], [https://www.ebi.ac.uk/pdbsum/3vb8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vb8 ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vb8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vb8 OCA], [https://pdbe.org/3vb8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vb8 RCSB], [https://www.ebi.ac.uk/pdbsum/3vb8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vb8 ProSAT]</span></td></tr>
	</table>		</table>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	While there has been considerable progress in designing protein-protein interactions, the design of proteins that bind polar surfaces is an unmet challenge. We describe the computational design of a protein that binds the acidic active site of hen egg lysozyme and inhibits the enzyme. The design process starts with two polar amino acids that fit deep into the enzyme active site, identifies a protein scaffold that supports these residues and is complementary in shape to the lysozyme active-site region, and finally optimizes the surrounding contact surface for high-affinity binding. Following affinity maturation, a protein designed using this method bound lysozyme with low nanomolar affinity, and a combination of NMR studies, crystallography, and knockout mutagenesis confirmed the designed binding surface and orientation. Saturation mutagenesis with selection and deep sequencing demonstrated that specific designed interactions extending well beyond the centrally grafted polar residues are critical for high-affinity binding.

	Computational Design of a Protein-Based Enzyme Inhibitor.,Procko E, Hedman R, Hamilton K, Seetharaman J, Fleishman SJ, Su M, Aramini J, Kornhaber G, Hunt JF, Tong L, Montelione GT, Baker D J Mol Biol. 2013 Jul 1. pii: S0022-2836(13)00430-0. doi:, 10.1016/j.jmb.2013.06.035. PMID:23827138<ref>PMID:23827138</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 3vb8" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Synthetic construct ~~sequences~~]]		[[Category: Synthetic construct]]
	[[Category: Acton~~, T B~~]]		[[Category: Acton TB]]
	[[Category: Baker, D]]		[[Category: Baker D]]
	[[Category: Ciccosanti, C]]		[[Category: Ciccosanti C]]
	[[Category: Everett~~, J K~~]]		[[Category: Everett JK]]
	[[Category: Hunt~~, J F~~]]		[[Category: Hunt JF]]
	[[Category: Montelione~~, G T]]~~		[[Category: Montelione GT]]
	~~[[Category: Structural genomic~~]]		[[Category: Procko E]]
	[[Category: Procko, E]]		[[Category: Sahdev S]]
	[[Category: Sahdev, S]]		[[Category: Seetharaman J]]
	[[Category: Seetharaman, J]]		[[Category: Su M]]
	[[Category: Su, M]]		[[Category: Tong L]]
	[[Category: Tong, L]]		[[Category: Xiao R]]
	[[Category: Xiao, R]]
	~~[[Category: De novo protein]]~~
	~~[[Category: Nesg]]~~
	~~[[Category: Psi-biology~~]]

OCA at 18:36, 27 July 2022

2022-07-27T18:36:22Z

← Older revision		Revision as of 18:36, 27 July 2022
Line 1:		Line 1:

	==Crystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR43==		==Crystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR43==
	<StructureSection load='3vb8' size='340' side='right' caption='[[3vb8]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='3vb8' size='340' side='right'caption='[[3vb8]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3vb8]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VB8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3VB8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3vb8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VB8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VB8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3vb8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vb8 OCA], [~~http~~://pdbe.org/3vb8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3vb8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3vb8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3vb8 ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vb8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vb8 OCA], [https://pdbe.org/3vb8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vb8 RCSB], [https://www.ebi.ac.uk/pdbsum/3vb8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vb8 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Synthetic construct sequences]]		[[Category: Synthetic construct sequences]]
	[[Category: Acton, T B]]		[[Category: Acton, T B]]

OCA at 15:57, 4 August 2016

2016-08-04T15:57:56Z

← Older revision		Revision as of 15:57, 4 August 2016
Line 1:		Line 1:

	==Crystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR43==		==Crystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR43==
	<StructureSection load='3vb8' size='340' side='right' caption='[[3vb8]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='3vb8' size='340' side='right' caption='[[3vb8]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3vb8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Synthetic_construct~~ Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VB8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VB8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3vb8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VB8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VB8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vb8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vb8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vb8 RCSB], [http://www.ebi.ac.uk/pdbsum/3vb8 PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vb8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vb8 OCA], [http://pdbe.org/3vb8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vb8 RCSB], [http://www.ebi.ac.uk/pdbsum/3vb8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vb8 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 15:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 3vb8" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Synthetic construct]]		[[Category: Synthetic construct sequences]]
	[[Category: Acton, T B]]		[[Category: Acton, T B]]
	[[Category: Baker, D]]		[[Category: Baker, D]]

OCA at 06:54, 21 December 2014

2014-12-21T06:54:39Z

← Older revision		Revision as of 06:54, 21 December 2014
Line 1:		Line 1:
	~~{{STRUCTURE_3vb8\| PDB=3vb8 \| SCENE= }}~~		==Crystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR43==
	===Crystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR43===		<StructureSection load='3vb8' size='340' side='right' caption='[[3vb8]], [[Resolution\|resolution]] 2.90Å' scene=''>
	~~{{ABSTRACT_PUBMED_23827138}}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[3vb8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VB8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VB8 FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
			<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vb8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vb8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vb8 RCSB], [http://www.ebi.ac.uk/pdbsum/3vb8 PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			While there has been considerable progress in designing protein-protein interactions, the design of proteins that bind polar surfaces is an unmet challenge. We describe the computational design of a protein that binds the acidic active site of hen egg lysozyme and inhibits the enzyme. The design process starts with two polar amino acids that fit deep into the enzyme active site, identifies a protein scaffold that supports these residues and is complementary in shape to the lysozyme active-site region, and finally optimizes the surrounding contact surface for high-affinity binding. Following affinity maturation, a protein designed using this method bound lysozyme with low nanomolar affinity, and a combination of NMR studies, crystallography, and knockout mutagenesis confirmed the designed binding surface and orientation. Saturation mutagenesis with selection and deep sequencing demonstrated that specific designed interactions extending well beyond the centrally grafted polar residues are critical for high-affinity binding.

	~~==About this Structure==~~		Computational Design of a Protein-Based Enzyme Inhibitor.,Procko E, Hedman R, Hamilton K, Seetharaman J, Fleishman SJ, Su M, Aramini J, Kornhaber G, Hunt JF, Tong L, Montelione GT, Baker D J Mol Biol. 2013 Jul 1. pii: S0022-2836(13)00430-0. doi:, 10.1016/j.jmb.2013.06.035. PMID:23827138<ref>PMID:23827138</ref>
	~~[[3vb8]] is~~ a ~~2 chain structure with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org~~/~~wiki/Synthetic_construct Synthetic construct]~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.ac.~~il/oca-bin~~/~~ocashort?id=3VB8 OCA].~~

	==~~Reference~~==		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	~~<ref group="xtra">PMID:023827138</ref>~~<references ~~group="xtra"~~/><~~references~~/>		</div>
			== References ==
			<references/>
			__TOC__
			</StructureSection>
	[[Category: Synthetic construct]]		[[Category: Synthetic construct]]
	[[Category: Acton, T B.]]		[[Category: Acton, T B]]
	[[Category: Baker, D.]]		[[Category: Baker, D]]
	[[Category: Ciccosanti, C.]]		[[Category: Ciccosanti, C]]
	[[Category: Everett, J K.]]		[[Category: Everett, J K]]
	[[Category: Hunt, J F.]]		[[Category: Hunt, J F]]
	[[Category: Montelione, G T.]]		[[Category: Montelione, G T]]
	[[Category: ~~NESG, Northeast~~ Structural ~~Genomics Consortium.~~]]		[[Category: Structural genomic]]
	[[Category: Procko, E.]]		[[Category: Procko, E]]
	[[Category: Sahdev, S.]]		[[Category: Sahdev, S]]
	[[Category: Seetharaman, J.]]		[[Category: Seetharaman, J]]
	[[Category: Su, M.]]		[[Category: Su, M]]
	[[Category: Tong, L.]]		[[Category: Tong, L]]
	[[Category: Xiao, R.]]		[[Category: Xiao, R]]
	[[Category: De novo protein]]		[[Category: De novo protein]]
	[[Category: Nesg]]		[[Category: Nesg]]
	~~[[Category: Northeast structural genomics consortium]]~~
	[[Category: Psi-biology]]		[[Category: Psi-biology]]
	~~[[Category: Structural genomic]]~~

OCA at 11:28, 24 July 2013

2013-07-24T11:28:33Z

← Older revision		Revision as of 11:28, 24 July 2013
Line 1:		Line 1:
	{{STRUCTURE_3vb8\| PDB=3vb8 \| SCENE= }}		{{STRUCTURE_3vb8\| PDB=3vb8 \| SCENE= }}
	===Crystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR43===		===Crystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR43===
			{{ABSTRACT_PUBMED_23827138}}

	==About this Structure==		==About this Structure==
	[[3vb8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VB8 OCA].		[[3vb8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VB8 OCA].

			==Reference==
			<ref group="xtra">PMID:023827138</ref><references group="xtra"/><references/>
	[[Category: Synthetic construct]]		[[Category: Synthetic construct]]
	[[Category: Acton, T B.]]		[[Category: Acton, T B.]]

OCA at 14:24, 10 July 2013

2013-07-10T14:24:09Z

@@ Line 1: / Line 1: @@
 {{STRUCTURE_3vb8|  PDB=3vb8  |  SCENE=  }}
 ===Crystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR43===
 ==About this Structure==

OCA at 07:52, 6 June 2012

2012-06-06T07:52:15Z

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+[[Image:3vb8.jpg|left|200px]]
-The entry 3vb8 is ON HOLD  until sometime in the future
+<!--
-Authors: Seetharaman, J., Su, M., Nivon, L., Baker, D., Bjelic, S., Ciccosanti, C., Sahdev, S., Xiao, R., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)
+===Crystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR43===
-Description: Crystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR43

OCA at 05:28, 23 May 2012

2012-05-23T05:28:50Z

← Older revision		Revision as of 05:28, 23 May 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 3vb8 is ON HOLD		The entry 3vb8 is ON HOLD until sometime in the future

	Authors: Seetharaman, J., Su, M., Nivon, L., Baker, D., Bjelic, S., Ciccosanti, C., Sahdev, S., Xiao, R., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)		Authors: Seetharaman, J., Su, M., Nivon, L., Baker, D., Bjelic, S., Ciccosanti, C., Sahdev, S., Xiao, R., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

	Description: Crystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR43		Description: Crystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR43

OCA: Protected "3vb8" [edit=sysop:move=sysop]

2012-01-11T06:00:06Z

Protected "3vb8" [edit=sysop:move=sysop]

← Older revision	Revision as of 06:00, 11 January 2012
(No difference)

OCA: New page: '''Unreleased structure''' The entry 3vb8 is ON HOLD Authors: Seetharaman, J., Su, M., Nivon, L., Baker, D., Bjelic, S., Ciccosanti, C., Sahdev, S., Xiao, R., Everett, J.K., Acton, T.B....

2012-01-11T06:00:05Z

New page: '''Unreleased structure''' The entry 3vb8 is ON HOLD Authors: Seetharaman, J., Su, M., Nivon, L., Baker, D., Bjelic, S., Ciccosanti, C., Sahdev, S., Xiao, R., Everett, J.K., Acton, T.B....

New page

'''Unreleased structure'''

The entry 3vb8 is ON HOLD

Authors: Seetharaman, J., Su, M., Nivon, L., Baker, D., Bjelic, S., Ciccosanti, C., Sahdev, S., Xiao, R., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Description: Crystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR43