2ny6 - Revision history

OCA at 10:26, 30 August 2023

2023-08-30T10:26:19Z

←Older revision		Revision as of 10:26, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2ny6' size='340' side='right'caption='[[2ny6]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2ny6' size='340' side='right'caption='[[2ny6]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ny6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~9hiv1 9hiv1~~] and [https://en.wikipedia.org/wiki/Human ~~Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NY6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NY6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ny6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NY6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NY6 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GLC:ALPHA~~-~~D-GLUCOSE'>GLC</scene>~~, ~~<scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</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]] 2.8Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1gc1\|1gc1]], [[1rzj\|1rzj]], [[1rzk\|1rzk]], [[2nxy\|2nxy]], [[2nxz\|2nxz]], [[2ny0\|2ny0]], [[2ny1\|2ny1]], [[2ny2\|2ny2]], [[2ny3\|2ny3]], [[2ny4\|2ny4]], [[2ny5\|2ny5]], [[2ny7\|2ny7]]~~</~~div~~><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene></td></tr>
-	<~~tr id~~='~~gene~~'><~~td class="sblockLbl"~~><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">CD4 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=2ny6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ny6 OCA], [https://pdbe.org/2ny6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ny6 RCSB], [https://www.ebi.ac.uk/pdbsum/2ny6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ny6 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=2ny6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ny6 OCA], [https://pdbe.org/2ny6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ny6 RCSB], [https://www.ebi.ac.uk/pdbsum/2ny6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ny6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~CD4_HUMAN CD4_HUMAN~~]~~] Accessory protein for MHC class-II antigen/T-cell receptor interaction. May regulate T-cell activation. Induces the aggregation of lipid rafts.~~	+	[https://www.uniprot.org/uniprot/Q8Q7Z9_9HIV1 Q8Q7Z9_9HIV1]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 40:		Line 39:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Human]]	+	[[Category: Homo sapiens]]
		+	[[Category: Human immunodeficiency virus 1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arthos, J]]	+	[[Category: Arthos J]]
-	[[Category: Burton~~, D R~~]]	+	[[Category: Burton DR]]
-	[[Category: Dey, B]]	+	[[Category: Dey B]]
-	[[Category: Dimitrov~~, D S~~]]	+	[[Category: Dimitrov DS]]
-	[[Category: Hessell~~, A J~~]]	+	[[Category: Hessell AJ]]
-	[[Category: Kwong~~, P D~~]]	+	[[Category: Kwong PD]]
-	[[Category: Nabel~~, G J~~]]	+	[[Category: Nabel GJ]]
-	[[Category: ~~Ryk, D Van~~]]	+	[[Category: Sodroski J]]
-	[[Category: ~~Sodroski, J~~]]	+	[[Category: Van Ryk D]]
-	[[Category: Wyatt, R]]	+	[[Category: Wyatt R]]
-	[[Category: Xiang~~, S H~~]]	+	[[Category: Xiang SH]]
-	[[Category: Xu, L]]	+	[[Category: Xu L]]
-	[[Category: Yang, X]]	+	[[Category: Yang X]]
-	[[Category: Zhang~~, M Y~~]]	+	[[Category: Zhang MY]]
-	[[Category: Zhou, T]]	+	[[Category: Zhou T]]
-	[[Category: Zwick~~, M B]]~~	+	[[Category: Zwick MB]]
-	~~[[Category: Antibody]]~~	+
-	~~[[Category: Cd4]]~~	+
-	~~[[Category: Gp120]]~~	+
-	~~[[Category: Hiv]]~~	+
-	~~[[Category: Viral protein-immune system complex~~]]	+

OCA at 15:54, 8 June 2021

2021-06-08T15:54:42Z

←Older revision		Revision as of 15:54, 8 June 2021
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	==HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, I109C, T123C, T257S, V275C,S334A, S375W, Q428C, G431C) Complexed with CD4 and Antibody 17b==		==HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, I109C, T123C, T257S, V275C,S334A, S375W, Q428C, G431C) Complexed with CD4 and Antibody 17b==
-	<StructureSection load='2ny6' size='340' side='right' caption='[[2ny6]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='2ny6' size='340' side='right'caption='[[2ny6]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ny6]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/9hiv1 9hiv1] and [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NY6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2NY6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ny6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/9hiv1 9hiv1] and [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NY6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NY6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=~~SUC~~:~~SUCROSE~~'>~~SUC~~</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gc1\|1gc1]], [[1rzj\|1rzj]], [[1rzk\|1rzk]], [[2nxy\|2nxy]], [[2nxz\|2nxz]], [[2ny0\|2ny0]], [[2ny1\|2ny1]], [[2ny2\|2ny2]], [[2ny3\|2ny3]], [[2ny4\|2ny4]], [[2ny5\|2ny5]], [[2ny7\|2ny7]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1gc1\|1gc1]], [[1rzj\|1rzj]], [[1rzk\|1rzk]], [[2nxy\|2nxy]], [[2nxz\|2nxz]], [[2ny0\|2ny0]], [[2ny1\|2ny1]], [[2ny2\|2ny2]], [[2ny3\|2ny3]], [[2ny4\|2ny4]], [[2ny5\|2ny5]], [[2ny7\|2ny7]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CD4 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CD4 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=2ny6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ny6 OCA], [~~http~~://pdbe.org/2ny6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2ny6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2ny6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2ny6 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=2ny6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ny6 OCA], [https://pdbe.org/2ny6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ny6 RCSB], [https://www.ebi.ac.uk/pdbsum/2ny6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ny6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CD4_HUMAN CD4_HUMAN]] Accessory protein for MHC class-II antigen/T-cell receptor interaction. May regulate T-cell activation. Induces the aggregation of lipid rafts.	+	[[https://www.uniprot.org/uniprot/CD4_HUMAN CD4_HUMAN]] Accessory protein for MHC class-II antigen/T-cell receptor interaction. May regulate T-cell activation. Induces the aggregation of lipid rafts.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ny/2ny6_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ny/2ny6_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[CD4\|CD4]]	+	*[[Antibody 3D structures\|Antibody 3D structures]]
-	*[[3D structures of antibody\|3D structures of antibody]]	+	*[[CD4 3D structures\|CD4 3D structures]]
		+	*[[Gp120 3D structures\|Gp120 3D structures]]
		+	*[[3D structures of human antibody\|3D structures of human antibody]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 41:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Arthos, J]]		[[Category: Arthos, J]]
	[[Category: Burton, D R]]		[[Category: Burton, D R]]

OCA at 08:44, 18 October 2017

2017-10-18T08:44:44Z

←Older revision		Revision as of 08:44, 18 October 2017
Line 1:		Line 1:
		+
	==HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, I109C, T123C, T257S, V275C,S334A, S375W, Q428C, G431C) Complexed with CD4 and Antibody 17b==		==HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, I109C, T123C, T257S, V275C,S334A, S375W, Q428C, G431C) Complexed with CD4 and Antibody 17b==
	<StructureSection load='2ny6' size='340' side='right' caption='[[2ny6]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2ny6' size='340' side='right' caption='[[2ny6]], [[Resolution\|resolution]] 2.80Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gc1\|1gc1]], [[1rzj\|1rzj]], [[1rzk\|1rzk]], [[2nxy\|2nxy]], [[2nxz\|2nxz]], [[2ny0\|2ny0]], [[2ny1\|2ny1]], [[2ny2\|2ny2]], [[2ny3\|2ny3]], [[2ny4\|2ny4]], [[2ny5\|2ny5]], [[2ny7\|2ny7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gc1\|1gc1]], [[1rzj\|1rzj]], [[1rzk\|1rzk]], [[2nxy\|2nxy]], [[2nxz\|2nxz]], [[2ny0\|2ny0]], [[2ny1\|2ny1]], [[2ny2\|2ny2]], [[2ny3\|2ny3]], [[2ny4\|2ny4]], [[2ny5\|2ny5]], [[2ny7\|2ny7]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CD4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CD4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=2ny6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ny6 OCA], [http://pdbe.org/2ny6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ny6 RCSB], [http://www.ebi.ac.uk/pdbsum/2ny6 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=2ny6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ny6 OCA], [http://pdbe.org/2ny6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ny6 RCSB], [http://www.ebi.ac.uk/pdbsum/2ny6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ny6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 31:		Line 32:

	==See Also==		==See Also==
-	*[[Antibody\|Antibody]]
	*[[CD4\|CD4]]		*[[CD4\|CD4]]
-	*[[~~Gp120~~\|~~Gp120~~]]	+	*[[3D structures of antibody\|3D structures of antibody]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:24, 9 February 2016

2016-02-09T13:24:30Z

←Older revision		Revision as of 13:24, 9 February 2016
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ny6 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:39, 10 September 2015

2015-09-10T22:39:33Z

←Older revision		Revision as of 22:39, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2ny6' size='340' side='right' caption='[[2ny6]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2ny6' size='340' side='right' caption='[[2ny6]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ny6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~] and [http://en.wikipedia.org/wiki/~~Human_immunodeficiency_virus_1~~ Human ~~immunodeficiency virus 1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NY6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NY6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ny6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/9hiv1 9hiv1] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NY6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NY6 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gc1\|1gc1]], [[1rzj\|1rzj]], [[1rzk\|1rzk]], [[2nxy\|2nxy]], [[2nxz\|2nxz]], [[2ny0\|2ny0]], [[2ny1\|2ny1]], [[2ny2\|2ny2]], [[2ny3\|2ny3]], [[2ny4\|2ny4]], [[2ny5\|2ny5]], [[2ny7\|2ny7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gc1\|1gc1]], [[1rzj\|1rzj]], [[1rzk\|1rzk]], [[2nxy\|2nxy]], [[2nxz\|2nxz]], [[2ny0\|2ny0]], [[2ny1\|2ny1]], [[2ny2\|2ny2]], [[2ny3\|2ny3]], [[2ny4\|2ny4]], [[2ny5\|2ny5]], [[2ny7\|2ny7]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CD4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CD4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=2ny6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ny6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ny6 RCSB], [http://www.ebi.ac.uk/pdbsum/2ny6 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=2ny6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ny6 OCA], [http://pdbe.org/2ny6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ny6 RCSB], [http://www.ebi.ac.uk/pdbsum/2ny6 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 2ny6" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	~~[[Category: Homo sapiens]]~~	+	[[Category: Human]]
-	[[Category: Human ~~immunodeficiency virus 1~~]]	+
	[[Category: Arthos, J]]		[[Category: Arthos, J]]
	[[Category: Burton, D R]]		[[Category: Burton, D R]]

OCA at 07:04, 25 December 2014

2014-12-25T07:04:53Z

←Older revision		Revision as of 07:04, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ny6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NY6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NY6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ny6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NY6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NY6 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gc1\|1gc1]], [[1rzj\|1rzj]], [[1rzk\|1rzk]], [[2nxy\|2nxy]], [[2nxz\|2nxz]], [[2ny0\|2ny0]], [[2ny1\|2ny1]], [[2ny2\|2ny2]], [[2ny3\|2ny3]], [[2ny4\|2ny4]], [[2ny5\|2ny5]], [[2ny7\|2ny7]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gc1\|1gc1]], [[1rzj\|1rzj]], [[1rzk\|1rzk]], [[2nxy\|2nxy]], [[2nxz\|2nxz]], [[2ny0\|2ny0]], [[2ny1\|2ny1]], [[2ny2\|2ny2]], [[2ny3\|2ny3]], [[2ny4\|2ny4]], [[2ny5\|2ny5]], [[2ny7\|2ny7]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CD4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CD4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ny6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ny6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ny6 RCSB], [http://www.ebi.ac.uk/pdbsum/2ny6 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=2ny6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ny6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ny6 RCSB], [http://www.ebi.ac.uk/pdbsum/2ny6 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CD4_HUMAN CD4_HUMAN]] Accessory protein for MHC class-II antigen/T-cell receptor interaction. May regulate T-cell activation. Induces the aggregation of lipid rafts.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 39:
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Human immunodeficiency virus 1]]		[[Category: Human immunodeficiency virus 1]]
-	[[Category: Arthos, J.]]	+	[[Category: Arthos, J]]
-	[[Category: Burton, D R.]]	+	[[Category: Burton, D R]]
-	[[Category: Dey, B.]]	+	[[Category: Dey, B]]
-	[[Category: Dimitrov, D S.]]	+	[[Category: Dimitrov, D S]]
-	[[Category: Hessell, A J.]]	+	[[Category: Hessell, A J]]
-	[[Category: Kwong, P D.]]	+	[[Category: Kwong, P D]]
-	[[Category: Nabel, G J.]]	+	[[Category: Nabel, G J]]
-	[[Category: Ryk, D Van.]]	+	[[Category: Ryk, D Van]]
-	[[Category: Sodroski, J.]]	+	[[Category: Sodroski, J]]
-	[[Category: Wyatt, R.]]	+	[[Category: Wyatt, R]]
-	[[Category: Xiang, S H.]]	+	[[Category: Xiang, S H]]
-	[[Category: Xu, L.]]	+	[[Category: Xu, L]]
-	[[Category: Yang, X.]]	+	[[Category: Yang, X]]
-	[[Category: Zhang, M Y.]]	+	[[Category: Zhang, M Y]]
-	[[Category: Zhou, T.]]	+	[[Category: Zhou, T]]
-	[[Category: Zwick, M B.]]	+	[[Category: Zwick, M B]]
	[[Category: Antibody]]		[[Category: Antibody]]
	[[Category: Cd4]]		[[Category: Cd4]]

OCA at 18:14, 30 September 2014

2014-09-30T18:14:34Z

←Older revision		Revision as of 18:14, 30 September 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_2ny6\| PDB=2ny6 \| SCENE= }}~~	+	==HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, I109C, T123C, T257S, V275C,S334A, S375W, Q428C, G431C) Complexed with CD4 and Antibody 17b==
-	===HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, I109C, T123C, T257S, V275C,S334A, S375W, Q428C, G431C) Complexed with CD4 and Antibody 17b===	+	<StructureSection load='2ny6' size='340' side='right' caption='[[2ny6]], [[Resolution\|resolution]] 2.80Å' scene=''>
-	~~{{ABSTRACT_PUBMED_17301785}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2ny6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NY6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NY6 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gc1\|1gc1]], [[1rzj\|1rzj]], [[1rzk\|1rzk]], [[2nxy\|2nxy]], [[2nxz\|2nxz]], [[2ny0\|2ny0]], [[2ny1\|2ny1]], [[2ny2\|2ny2]], [[2ny3\|2ny3]], [[2ny4\|2ny4]], [[2ny5\|2ny5]], [[2ny7\|2ny7]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CD4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ny6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ny6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ny6 RCSB], [http://www.ebi.ac.uk/pdbsum/2ny6 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ny/2ny6_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The remarkable diversity, glycosylation and conformational flexibility of the human immunodeficiency virus type 1 (HIV-1) envelope (Env), including substantial rearrangement of the gp120 glycoprotein upon binding the CD4 receptor, allow it to evade antibody-mediated neutralization. Despite this complexity, the HIV-1 Env must retain conserved determinants that mediate CD4 binding. To evaluate how these determinants might provide opportunities for antibody recognition, we created variants of gp120 stabilized in the CD4-bound state, assessed binding of CD4 and of receptor-binding-site antibodies, and determined the structure at 2.3 A resolution of the broadly neutralizing antibody b12 in complex with gp120. b12 binds to a conformationally invariant surface that overlaps a distinct subset of the CD4-binding site. This surface is involved in the metastable attachment of CD4, before the gp120 rearrangement required for stable engagement. A site of vulnerability, related to a functional requirement for efficient association with CD4, can therefore be targeted by antibody to neutralize HIV-1.

-	~~==About this Structure==~~	+	Structural definition of a conserved neutralization epitope on HIV-1 gp120.,Zhou T, Xu L, Dey B, Hessell AJ, Van Ryk D, Xiang SH, Yang X, Zhang MY, Zwick MB, Arthos J, Burton DR, Dimitrov DS, Sodroski J, Wyatt R, Nabel GJ, Kwong PD Nature. 2007 Feb 15;445(7129):732-7. PMID:17301785<ref>PMID:17301785</ref>
-	~~[[2ny6]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens] and [http~~:~~//en~~.~~wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=2NY6 OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
		+	*[[Antibody\|Antibody]]
		+	*[[CD4\|CD4]]
	*[[Gp120\|Gp120]]		*[[Gp120\|Gp120]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:017301785<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Human immunodeficiency virus 1]]		[[Category: Human immunodeficiency virus 1]]

OCA at 09:21, 11 March 2013

2013-03-11T09:21:22Z

←Older revision		Revision as of 09:21, 11 March 2013
Line 1:		Line 1:
-	[[Image:2ny6.png\|left\|200px]]
-
	{{STRUCTURE_2ny6\| PDB=2ny6 \| SCENE= }}		{{STRUCTURE_2ny6\| PDB=2ny6 \| SCENE= }}
-
	===HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, I109C, T123C, T257S, V275C,S334A, S375W, Q428C, G431C) Complexed with CD4 and Antibody 17b===		===HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, I109C, T123C, T257S, V275C,S334A, S375W, Q428C, G431C) Complexed with CD4 and Antibody 17b===
-
	{{ABSTRACT_PUBMED_17301785}}		{{ABSTRACT_PUBMED_17301785}}

OCA: Protected "2ny6" [edit=sysop:move=sysop]

2013-01-07T18:05:43Z

Protected "2ny6" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:05, 7 January 2013

OCA at 18:05, 7 January 2013

2013-01-07T18:05:41Z

←Older revision		Revision as of 18:05, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2ny6.png\|left\|200px]]		[[Image:2ny6.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2ny6", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
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	{{STRUCTURE_2ny6\| PDB=2ny6 \| SCENE= }}		{{STRUCTURE_2ny6\| PDB=2ny6 \| SCENE= }}

	===HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, I109C, T123C, T257S, V275C,S334A, S375W, Q428C, G431C) Complexed with CD4 and Antibody 17b===		===HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, I109C, T123C, T257S, V275C,S334A, S375W, Q428C, G431C) Complexed with CD4 and Antibody 17b===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17301785}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17301785 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17301785}}		{{ABSTRACT_PUBMED_17301785}}
-
-	==Disease==
-	Known disease associated with this structure: CD4 lymphocyte deficiency OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=186940 186940]], Lupus erythematosus, susceptibility to OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=186940 186940]]

	==About this Structure==		==About this Structure==
-	~~2NY6~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NY6 OCA].	+	[[2ny6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NY6 OCA].
		+
		+	==See Also==
		+	*[[Gp120\|Gp120]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17301785~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017301785</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Human immunodeficiency virus 1]]		[[Category: Human immunodeficiency virus 1]]
Line 49:		Line 37:
	[[Category: Gp120]]		[[Category: Gp120]]
	[[Category: Hiv]]		[[Category: Hiv]]
-		+	[[Category: Viral protein-immune system complex]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 10:06:17 2009''~~	+