4ybl - Revision history

OCA at 07:56, 27 September 2023

OCA — Wed, 27 Sep 2023 07:56:13 GMT

←Older revision		Revision as of 07:56, 27 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ybl]] is a 6 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=4YBL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YBL FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ybl]] is a 6 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=4YBL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YBL FirstGlance]. <br>
-	</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=4ybl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybl OCA], [https://pdbe.org/4ybl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ybl RCSB], [https://www.ebi.ac.uk/pdbsum/4ybl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ybl ProSAT]</span></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]] 3.1Å</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=4ybl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybl OCA], [https://pdbe.org/4ybl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ybl RCSB], [https://www.ebi.ac.uk/pdbsum/4ybl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ybl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 08:07, 3 May 2023

OCA — Wed, 03 May 2023 08:07:15 GMT

←Older revision		Revision as of 08:07, 3 May 2023
Line 3:		Line 3:
	<StructureSection load='4ybl' size='340' side='right'caption='[[4ybl]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='4ybl' size='340' side='right'caption='[[4ybl]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ybl]] is a 6 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=4YBL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4YBL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ybl]] is a 6 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=4YBL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YBL FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tnm\|3tnm]], [[4rqh\|4rqh]], [[4h8w\|4h8w]], [[4yc2\|4yc2]]</td></tr>~~	+	</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=4ybl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybl OCA], [https://pdbe.org/4ybl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ybl RCSB], [https://www.ebi.ac.uk/pdbsum/4ybl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ybl ProSAT]</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=4ybl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybl OCA], [~~http~~://pdbe.org/4ybl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ybl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ybl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ybl ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0M3KKW9_9HIV1 A0A0M3KKW9_9HIV1]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
	*[[Gp120 3D structures\|Gp120 3D structures]]		*[[Gp120 3D structures\|Gp120 3D structures]]
		+	*[[3D structures of human antibody\|3D structures of human antibody]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Human]]	+	[[Category: Homo sapiens]]
		+	[[Category: Human immunodeficiency virus 1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gohain, N]]	+	[[Category: Gohain N]]
-	[[Category: Pazgier, M]]	+	[[Category: Pazgier M]]
-	[[Category: Tolbert~~, W D]]~~	+	[[Category: Tolbert WD]]
-	~~[[Category: Adcc]]~~	+
-	~~[[Category: Anti-hiv-1 env antibody a32]]~~	+
-	~~[[Category: Cd4i antibody]]~~	+
-	~~[[Category: Hiv-1 env]]~~	+
-	~~[[Category: Non-neutralizing]]~~	+
-	~~[[Category: Viral glycoprotein gp120]]~~	+
-	~~[[Category: Viral protein-immune system complex~~]]	+

OCA at 07:55, 4 March 2020

OCA — Wed, 04 Mar 2020 07:55:05 GMT

←Older revision		Revision as of 07:55, 4 March 2020
Line 1:		Line 1:

	==Crystal structure of the stabilized inner domain of clade A/E HIV-1 gp120 in complex with the ADCC mediating ANTI-HIV-1 antibody A32==		==Crystal structure of the stabilized inner domain of clade A/E HIV-1 gp120 in complex with the ADCC mediating ANTI-HIV-1 antibody A32==
-	<StructureSection load='4ybl' size='340' side='right' caption='[[4ybl]], [[Resolution\|resolution]] 3.10Å' scene=''>	+	<StructureSection load='4ybl' size='340' side='right'caption='[[4ybl]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ybl]] is a 6 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=4YBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YBL FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ybl]] is a 6 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=4YBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YBL FirstGlance]. <br>
Line 18:		Line 18:

	==See Also==		==See Also==
-	*[[3D structures ~~of antibody~~\|3D structures ~~of antibody~~]]	+	*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[Gp120 3D structures\|Gp120 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Gohain, N]]		[[Category: Gohain, N]]
	[[Category: Pazgier, M]]		[[Category: Pazgier, M]]

OCA at 09:06, 1 November 2017

OCA — Wed, 01 Nov 2017 09:06:47 GMT

←Older revision		Revision as of 09:06, 1 November 2017
Line 3:		Line 3:
	<StructureSection load='4ybl' size='340' side='right' caption='[[4ybl]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='4ybl' size='340' side='right' caption='[[4ybl]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ybl]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YBL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ybl]] is a 6 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=4YBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YBL FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tnm\|3tnm]], [[4rqh\|4rqh]], [[4h8w\|4h8w]], [[4yc2\|4yc2]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tnm\|3tnm]], [[4rqh\|4rqh]], [[4h8w\|4h8w]], [[4yc2\|4yc2]]</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=4ybl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybl OCA], [http://pdbe.org/4ybl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ybl RCSB], [http://www.ebi.ac.uk/pdbsum/4ybl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ybl ProSAT]</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=4ybl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybl OCA], [http://pdbe.org/4ybl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ybl RCSB], [http://www.ebi.ac.uk/pdbsum/4ybl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ybl ProSAT]</span></td></tr>
Line 16:		Line 16:
	</div>		</div>
	<div class="pdbe-citations 4ybl" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4ybl" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[3D structures of antibody\|3D structures of antibody]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Gohain, N]]		[[Category: Gohain, N]]
	[[Category: Pazgier, M]]		[[Category: Pazgier, M]]

OCA at 02:32, 13 July 2016

OCA — Wed, 13 Jul 2016 02:32:49 GMT

←Older revision		Revision as of 02:32, 13 July 2016
Line 5:		Line 5:
	<table><tr><td colspan='2'>[[4ybl]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YBL FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ybl]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YBL FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tnm\|3tnm]], [[4rqh\|4rqh]], [[4h8w\|4h8w]], [[4yc2\|4yc2]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tnm\|3tnm]], [[4rqh\|4rqh]], [[4h8w\|4h8w]], [[4yc2\|4yc2]]</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=4ybl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybl OCA], [http://pdbe.org/4ybl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ybl RCSB], [http://www.ebi.ac.uk/pdbsum/4ybl 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=4ybl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybl OCA], [http://pdbe.org/4ybl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ybl RCSB], [http://www.ebi.ac.uk/pdbsum/4ybl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ybl ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 15:41, 23 June 2016

OCA — Thu, 23 Jun 2016 15:41:22 GMT

←Older revision		Revision as of 15:41, 23 June 2016
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	<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=4ybl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybl OCA], [http://pdbe.org/4ybl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ybl RCSB], [http://www.ebi.ac.uk/pdbsum/4ybl 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=4ybl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybl OCA], [http://pdbe.org/4ybl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ybl RCSB], [http://www.ebi.ac.uk/pdbsum/4ybl PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Evidence supports a role of antibody-dependent cellular cytotoxicity (ADCC) toward transitional epitopes in the first and second constant (C1-C2) regions of gp120 (A32-like epitopes) in preventing HIV-1 infection and in vaccine-induced protection. Here, we describe the first successful attempt at isolating the inner domain (ID) of gp120 as an independent molecule that encapsulates the A32-like region within a minimal structural unit of the HIV-1 Env. Through structure-based design, we developed ID2, which consists of the ID expressed independently of the outer domain and stabilized in the CD4-bound conformation by an inter-layer disulfide bond. ID2 expresses C1-C2 epitopes in the context of CD4-triggered full-length gp120 but without any known neutralizing epitope present. Thus, ID2 represents a novel probe for the analysis and/or selective induction of antibody responses to the A32 epitope region. We also present the crystal structure of ID2 complexed with mAb A32, which defines its epitope.
		+
		+	Paring Down HIV Env: Design and Crystal Structure of a Stabilized Inner Domain of HIV-1 gp120 Displaying a Major ADCC Target of the A32 Region.,Tolbert WD, Gohain N, Veillette M, Chapleau JP, Orlandi C, Visciano ML, Ebadi M, DeVico AL, Fouts TR, Finzi A, Lewis GK, Pazgier M Structure. 2016 May 3;24(5):697-709. doi: 10.1016/j.str.2016.03.005. Epub 2016, Mar 31. PMID:27041594<ref>PMID:27041594</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4ybl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 15:20, 2 March 2016

OCA — Wed, 02 Mar 2016 15:20:01 GMT

←Older revision		Revision as of 15:20, 2 March 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 4ybl is ON HOLD until Paper Publication~~	+	==Crystal structure of the stabilized inner domain of clade A/E HIV-1 gp120 in complex with the ADCC mediating ANTI-HIV-1 antibody A32==
-		+	<StructureSection load='4ybl' size='340' side='right' caption='[[4ybl]], [[Resolution\|resolution]] 3.10Å' scene=''>
-	~~Authors: Tolbert, W.D., Gohain, N., Pazgier, M.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4ybl]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YBL FirstGlance]. <br>
-	~~Description:~~ Crystal structure of the stabilized inner domain of clade A/E HIV-1 gp120 in complex with the ADCC mediating ANTI-HIV-1 antibody A32	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tnm\|3tnm]], [[4rqh\|4rqh]], [[4h8w\|4h8w]], [[4yc2\|4yc2]]</td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=4ybl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybl OCA], [http://pdbe.org/4ybl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ybl RCSB], [http://www.ebi.ac.uk/pdbsum/4ybl PDBsum]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Gohain, N]]
	[[Category: Pazgier, M]]		[[Category: Pazgier, M]]
-	[[Category: Tolbert, W.D]]	+	[[Category: Tolbert, W D]]
-	[[Category: ~~Gohain, N~~]]	+	[[Category: Adcc]]
		+	[[Category: Anti-hiv-1 env antibody a32]]
		+	[[Category: Cd4i antibody]]
		+	[[Category: Hiv-1 env]]
		+	[[Category: Non-neutralizing]]
		+	[[Category: Viral glycoprotein gp120]]
		+	[[Category: Viral protein-immune system complex]]

OCA at 10:28, 11 March 2015

OCA — Wed, 11 Mar 2015 10:28:26 GMT

←Older revision		Revision as of 10:28, 11 March 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4ybl is ON HOLD	+	The entry 4ybl is ON HOLD until Paper Publication

	Authors: Tolbert, W.D., Gohain, N., Pazgier, M.		Authors: Tolbert, W.D., Gohain, N., Pazgier, M.

OCA: Protected "4ybl" [edit=sysop:move=sysop]

OCA — Wed, 25 Feb 2015 12:57:16 GMT

Protected "4ybl" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:57, 25 February 2015

OCA: New page: '''Unreleased structure''' The entry 4ybl is ON HOLD Authors: Tolbert, W.D., Gohain, N., Pazgier, M. Description: Crystal structure of the stabilized inner domain of clade A/E HIV-1 gp...

OCA — Wed, 25 Feb 2015 12:57:14 GMT

New page: '''Unreleased structure''' The entry 4ybl is ON HOLD Authors: Tolbert, W.D., Gohain, N., Pazgier, M. Description: Crystal structure of the stabilized inner domain of clade A/E HIV-1 gp...

New page

'''Unreleased structure'''

The entry 4ybl is ON HOLD

Authors: Tolbert, W.D., Gohain, N., Pazgier, M.

Description: Crystal structure of the stabilized inner domain of clade A/E HIV-1 gp120 in complex with the ADCC mediating ANTI-HIV-1 antibody A32
[[Category: Unreleased Structures]]
[[Category: Pazgier, M]]
[[Category: Tolbert, W.D]]
[[Category: Gohain, N]]