6k0y - Revision history

OCA at 10:24, 22 November 2023

2023-11-22T10:24:58Z

←Older revision		Revision as of 10:24, 22 November 2023
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	<StructureSection load='6k0y' size='340' side='right'caption='[[6k0y]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='6k0y' size='340' side='right'caption='[[6k0y]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6k0y]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K0Y OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6K0Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k0y]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K0Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K0Y FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]] 1.7Å</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=6k0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k0y OCA], [~~http~~://pdbe.org/6k0y PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6k0y RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6k0y PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6k0y ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=6k0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k0y OCA], [https://pdbe.org/6k0y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k0y RCSB], [https://www.ebi.ac.uk/pdbsum/6k0y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k0y ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/PDCD1_HUMAN PDCD1_HUMAN]] Systemic lupus erythematosus;Multiple sclerosis. Systemic lupus erythematosus 2 (SLEB2) [MIM:[~~http~~://omim.org/entry/605218 605218]]: A chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys and serosal membranes. It is of unknown etiology, but is thought to represent a failure of the regulatory mechanisms of the autoimmune system. The disease is marked by a wide range of system dysfunctions, an elevated erythrocyte sedimentation rate, and the formation of LE cells in the blood or bone marrow. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.<ref>PMID:12402038</ref>	+	[https://www.uniprot.org/uniprot/PDCD1_HUMAN PDCD1_HUMAN] Systemic lupus erythematosus;Multiple sclerosis. Systemic lupus erythematosus 2 (SLEB2) [MIM:[https://omim.org/entry/605218 605218]: A chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys and serosal membranes. It is of unknown etiology, but is thought to represent a failure of the regulatory mechanisms of the autoimmune system. The disease is marked by a wide range of system dysfunctions, an elevated erythrocyte sedimentation rate, and the formation of LE cells in the blood or bone marrow. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.<ref>PMID:12402038</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PDCD1_HUMAN PDCD1_HUMAN]] Inhibitory cell surface receptor involved in the regulation of T-cell function during immunity and tolerance. Upon ligand binding, inhibits T-cell effector functions in an antigen-specific manner. Possible cell death inducer, in association with other factors.<ref>PMID:21276005</ref>	+	[https://www.uniprot.org/uniprot/PDCD1_HUMAN PDCD1_HUMAN] Inhibitory cell surface receptor involved in the regulation of T-cell function during immunity and tolerance. Upon ligand binding, inhibits T-cell effector functions in an antigen-specific manner. Possible cell death inducer, in association with other factors.<ref>PMID:21276005</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6k0y" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6k0y" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cell death protein 3D structures\|Cell death protein 3D structures]]
		+	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Liu~~, J X~~]]	+	[[Category: Liu JX]]
-	[[Category: Wang~~, G Q]]~~	+	[[Category: Wang GQ]]
-	~~[[Category: Immune checkpoint]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Pd-1 complex~~]]	+

OCA at 15:06, 11 December 2019

2019-12-11T15:06:00Z

←Older revision		Revision as of 15:06, 11 December 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6k0y is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Study of the interactions of a novel monoclonal antibody, mAb059c, with the hPD-1 receptor==
		+	<StructureSection load='6k0y' size='340' side='right'caption='[[6k0y]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6k0y]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K0Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K0Y FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=6k0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k0y OCA], [http://pdbe.org/6k0y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k0y RCSB], [http://www.ebi.ac.uk/pdbsum/6k0y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k0y ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/PDCD1_HUMAN PDCD1_HUMAN]] Systemic lupus erythematosus;Multiple sclerosis. Systemic lupus erythematosus 2 (SLEB2) [MIM:[http://omim.org/entry/605218 605218]]: A chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys and serosal membranes. It is of unknown etiology, but is thought to represent a failure of the regulatory mechanisms of the autoimmune system. The disease is marked by a wide range of system dysfunctions, an elevated erythrocyte sedimentation rate, and the formation of LE cells in the blood or bone marrow. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.<ref>PMID:12402038</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PDCD1_HUMAN PDCD1_HUMAN]] Inhibitory cell surface receptor involved in the regulation of T-cell function during immunity and tolerance. Upon ligand binding, inhibits T-cell effector functions in an antigen-specific manner. Possible cell death inducer, in association with other factors.<ref>PMID:21276005</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Programmed cell death 1 (PD-1) monoclonal antibodies have been approved by regulatory agencies for the treatment of various types of cancer, and the mechanism involves the restoration of T cell functions. We report herein the X-ray crystal structure of a fully human monoclonal antibody mAb059c fragment antigen-binding (Fab) in complex with the PD-1 extracellular domain (ECD) at a resolution of 1.70 A. Structural analysis indicates 1) an epitope, comprising fragments from the C'D, BC and FG loops of PD-1, contributes to mAb059c interaction, 2) an unique conformation of the C'D loop and a different orientation of R86 enabling the capture of PD-1 by the antibody complementarity determining region (CDR) and the formation of one salt-bridge contact - ASP101(HCDR3):ARG86(PD-1), and 3) the contact of FG with light chain (LC) CDR3 is maintained by a second salt-bridge and two backbone hydrogen bonds. Interface analysis reveals that N-glycosylation sites 49, 74 and 116 on PD-1 do not contact mAb059c; while N58 in the BC loop is recognized by mAb059c heavy chain CDR1 and CDR2. Mutation of N58 attenuated mAb059c binding to PD-1. These findings and the novel anti-PD-1 antibody will facilitate better understanding of the mechanisms of the molecular recognition of PD-1 receptor by anti-PD-1 mAb and, thereby, enable the development of new therapeutics with an expanded spectrum of efficacy for unmet medical needs.

-	~~Authors: Liu~~, J.X., Wang, G.Q.	+	Study of the interactions of a novel monoclonal antibody, mAb059c, with the hPD-1 receptor.,Liu J, Wang G, Liu L, Wu R, Wu Y, Fang C, Zhou X, Jiao J, Gu Y, Zhou H, Xie Z, Sun Z, Chen D, Dai K, Wang D, Tang W, Yang TTC Sci Rep. 2019 Nov 28;9(1):17830. doi: 10.1038/s41598-019-54231-w. PMID:31780710<ref>PMID:31780710</ref>

-	~~Description: Study~~ of the ~~interactions~~ of ~~a novel monoclonal antibody, mAb059c, with the hPD~~-~~1 receptor~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Liu, J.X]]	+	<div class="pdbe-citations 6k0y" style="background-color:#fffaf0;"></div>
-	[[Category: Wang, G.Q]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Liu, J X]]
		+	[[Category: Wang, G Q]]
		+	[[Category: Immune checkpoint]]
		+	[[Category: Immune system]]
		+	[[Category: Inhibitor]]
		+	[[Category: Pd-1 complex]]

OCA at 06:13, 4 December 2019

2019-12-04T06:13:23Z

←Older revision		Revision as of 06:13, 4 December 2019
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	Authors: Liu, J.X., Wang, G.Q.		Authors: Liu, J.X., Wang, G.Q.

-	Description: ~~Complex structure~~ of PD-1 ~~and Ab059c-Fab~~	+	Description: Study of the interactions of a novel monoclonal antibody, mAb059c, with the hPD-1 receptor
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Wang, G.Q]]
	[[Category: Liu, J.X]]		[[Category: Liu, J.X]]
		+	[[Category: Wang, G.Q]]

OCA at 20:56, 5 June 2019

2019-06-05T20:56:51Z

←Older revision		Revision as of 20:56, 5 June 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6k0y is ON HOLD	+	The entry 6k0y is ON HOLD until Paper Publication

	Authors: Liu, J.X., Wang, G.Q.		Authors: Liu, J.X., Wang, G.Q.

OCA: Protected "6k0y" [edit=sysop:move=sysop]

2019-05-21T05:40:38Z

Protected "6k0y" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:40, 21 May 2019

OCA: New page: '''Unreleased structure''' The entry 6k0y is ON HOLD Authors: Liu, J.X., Wang, G.Q. Description: Complex structure of PD-1 and Ab059c-Fab Category: Unreleased Structures [[Category...

2019-05-21T05:40:36Z

New page: '''Unreleased structure''' The entry 6k0y is ON HOLD Authors: Liu, J.X., Wang, G.Q. Description: Complex structure of PD-1 and Ab059c-Fab Category: Unreleased Structures [[Category...

New page

'''Unreleased structure'''

The entry 6k0y is ON HOLD

Authors: Liu, J.X., Wang, G.Q.

Description: Complex structure of PD-1 and Ab059c-Fab
[[Category: Unreleased Structures]]
[[Category: Wang, G.Q]]
[[Category: Liu, J.X]]