5i1j - Revision history

OCA at 08:20, 23 August 2023

OCA — Wed, 23 Aug 2023 08:20:08 GMT

←Older revision		Revision as of 08:20, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='5i1j' size='340' side='right'caption='[[5i1j]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5i1j' size='340' side='right'caption='[[5i1j]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i1j]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I1J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5I1J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i1j]] is a 2 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=5I1J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5I1J FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.5Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">[[5i15\|5i15]], [[5i16\|5i16]], [[5i17\|5i17]], [[5i18\|5i18]], [[5i19\|5i19]], [[5i1a\|5i1a]], [[5i1c\|5i1c]], [[5i1d\|5i1d]], [[5i1e\|5i1e]], [[5i1g\|5i1g]], [[5i1h\|5i1h]], [[5i1i\|5i1i]], [[5i1k\|5i1k]], [[5i1l\|5i1l]], [[4kmt\|4kmt]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5i1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i1j OCA], [~~http~~://pdbe.org/5i1j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5i1j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5i1j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5i1j 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=5i1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i1j OCA], [https://pdbe.org/5i1j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5i1j RCSB], [https://www.ebi.ac.uk/pdbsum/5i1j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5i1j ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gilliland, G]]	+	[[Category: Gilliland G]]
-	[[Category: Luo, J]]	+	[[Category: Luo J]]
-	[[Category: Malia, T]]	+	[[Category: Malia T]]
-	[[Category: Obmolova, G]]	+	[[Category: Obmolova G]]
-	[[Category: Teplyakov, A]]	+	[[Category: Teplyakov A]]
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Monoclonal antibody~~]]	+

OCA at 08:41, 27 May 2020

OCA — Wed, 27 May 2020 08:41:52 GMT

←Older revision		Revision as of 08:41, 27 May 2020
Line 1:		Line 1:

	==CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY IGHV5-51/IGKV3-11==		==CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY IGHV5-51/IGKV3-11==
-	<StructureSection load='5i1j' size='340' side='right' caption='[[5i1j]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='5i1j' size='340' side='right'caption='[[5i1j]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i1j]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I1J OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5I1J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i1j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I1J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5I1J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i15\|5i15]], [[5i16\|5i16]], [[5i17\|5i17]], [[5i18\|5i18]], [[5i19\|5i19]], [[5i1a\|5i1a]], [[5i1c\|5i1c]], [[5i1d\|5i1d]], [[5i1e\|5i1e]], [[5i1g\|5i1g]], [[5i1h\|5i1h]], [[5i1i\|5i1i]], [[5i1k\|5i1k]], [[5i1l\|5i1l]], [[4kmt\|4kmt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i15\|5i15]], [[5i16\|5i16]], [[5i17\|5i17]], [[5i18\|5i18]], [[5i19\|5i19]], [[5i1a\|5i1a]], [[5i1c\|5i1c]], [[5i1d\|5i1d]], [[5i1e\|5i1e]], [[5i1g\|5i1g]], [[5i1h\|5i1h]], [[5i1i\|5i1i]], [[5i1k\|5i1k]], [[5i1l\|5i1l]], [[4kmt\|4kmt]]</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=5i1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i1j OCA], [http://pdbe.org/5i1j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i1j RCSB], [http://www.ebi.ac.uk/pdbsum/5i1j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i1j ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5i1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i1j OCA], [http://pdbe.org/5i1j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i1j RCSB], [http://www.ebi.ac.uk/pdbsum/5i1j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i1j ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Gilliland, G]]		[[Category: Gilliland, G]]
	[[Category: Luo, J]]		[[Category: Luo, J]]

OCA at 18:28, 12 July 2016

OCA — Tue, 12 Jul 2016 18:28:54 GMT

←Older revision		Revision as of 18:28, 12 July 2016
Line 6:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i15\|5i15]], [[5i16\|5i16]], [[5i17\|5i17]], [[5i18\|5i18]], [[5i19\|5i19]], [[5i1a\|5i1a]], [[5i1c\|5i1c]], [[5i1d\|5i1d]], [[5i1e\|5i1e]], [[5i1g\|5i1g]], [[5i1h\|5i1h]], [[5i1i\|5i1i]], [[5i1k\|5i1k]], [[5i1l\|5i1l]], [[4kmt\|4kmt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i15\|5i15]], [[5i16\|5i16]], [[5i17\|5i17]], [[5i18\|5i18]], [[5i19\|5i19]], [[5i1a\|5i1a]], [[5i1c\|5i1c]], [[5i1d\|5i1d]], [[5i1e\|5i1e]], [[5i1g\|5i1g]], [[5i1h\|5i1h]], [[5i1i\|5i1i]], [[5i1k\|5i1k]], [[5i1l\|5i1l]], [[4kmt\|4kmt]]</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=5i1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i1j OCA], [http://pdbe.org/5i1j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i1j RCSB], [http://www.ebi.ac.uk/pdbsum/5i1j 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=5i1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i1j OCA], [http://pdbe.org/5i1j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i1j RCSB], [http://www.ebi.ac.uk/pdbsum/5i1j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i1j ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 15:26, 20 June 2016

OCA — Mon, 20 Jun 2016 15:26:00 GMT

←Older revision		Revision as of 15:26, 20 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5i1j is ~~ON HOLD until Paper~~ Publication	+	==CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY IGHV5-51/IGKV3-11==
		+	<StructureSection load='5i1j' size='340' side='right' caption='[[5i1j]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5i1j]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I1J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I1J FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i15\|5i15]], [[5i16\|5i16]], [[5i17\|5i17]], [[5i18\|5i18]], [[5i19\|5i19]], [[5i1a\|5i1a]], [[5i1c\|5i1c]], [[5i1d\|5i1d]], [[5i1e\|5i1e]], [[5i1g\|5i1g]], [[5i1h\|5i1h]], [[5i1i\|5i1i]], [[5i1k\|5i1k]], [[5i1l\|5i1l]], [[4kmt\|4kmt]]</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=5i1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i1j OCA], [http://pdbe.org/5i1j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i1j RCSB], [http://www.ebi.ac.uk/pdbsum/5i1j PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	To support antibody therapeutic development, the crystal structures of a set of 16 germline variants composed of 4 different kappa light chains paired with 4 different heavy chains have been determined. All four heavy chains of the antigen-binding fragments (Fabs) have the same complementarity-determining region (CDR) H3 that was reported in an earlier Fab structure. The structure analyses include comparisons of the overall structures, canonical structures of the CDRs and the VH:VL packing interactions. The CDR conformations for the most part are tightly clustered, especially for the ones with shorter lengths. The longer CDRs with tandem glycines or serines have more conformational diversity than the others. CDR H3, despite having the same amino acid sequence, exhibits the largest conformational diversity. About half of the structures have CDR H3 conformations similar to that of the parent; the others diverge significantly. One conclusion is that the CDR H3 conformations are influenced by both their amino acid sequence and their structural environment determined by the heavy and light chain pairing. The stem regions of 14 of the variant pairs are in the 'kinked' conformation, and only 2 are in the extended conformation. The packing of the VH and VL domains is consistent with our knowledge of antibody structure, and the tilt angles between these domains cover a range of 11 degrees. Two of 16 structures showed particularly large variations in the tilt angles when compared with the other pairings. The structures and their analyses provide a rich foundation for future antibody modeling and engineering efforts.

-	~~Authors:~~ Teplyakov, A., Obmolova, G., Malia~~, T.~~, Luo, J., Gilliland~~, G~~.	+	Structural diversity in a human antibody germline library.,Teplyakov A, Obmolova G, Malia TJ, Luo J, Muzammil S, Sweet R, Almagro JC, Gilliland GL MAbs. 2016 May 21:1-19. PMID:27210805<ref>PMID:27210805</ref>

-	~~Description: CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY IGHV5-51~~/~~IGKV3-11~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Malia, T]]~~	+	<div class="pdbe-citations 5i1j" style="background-color:#fffaf0;"></div>
-	~~[[Category: Teplyakov, A]]~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Gilliland, G]]		[[Category: Gilliland, G]]
-	[[Category: Obmolova, G]]
	[[Category: Luo, J]]		[[Category: Luo, J]]
		+	[[Category: Malia, T]]
		+	[[Category: Obmolova, G]]
		+	[[Category: Teplyakov, A]]
		+	[[Category: Immune system]]
		+	[[Category: Monoclonal antibody]]

OCA at 00:07, 11 May 2016

OCA — Wed, 11 May 2016 00:07:43 GMT

←Older revision		Revision as of 00:07, 11 May 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5i1j is ON HOLD	+	The entry 5i1j is ON HOLD until Paper Publication

	Authors: Teplyakov, A., Obmolova, G., Malia, T., Luo, J., Gilliland, G.		Authors: Teplyakov, A., Obmolova, G., Malia, T., Luo, J., Gilliland, G.

OCA: Protected "5i1j" [edit=sysop:move=sysop]

OCA — Sun, 21 Feb 2016 01:25:49 GMT

Protected "5i1j" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:25, 21 February 2016

OCA: New page: '''Unreleased structure''' The entry 5i1j is ON HOLD Authors: Teplyakov, A., Obmolova, G., Malia, T., Luo, J., Gilliland, G. Description: CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY I...

OCA — Sun, 21 Feb 2016 01:25:48 GMT

New page: '''Unreleased structure''' The entry 5i1j is ON HOLD Authors: Teplyakov, A., Obmolova, G., Malia, T., Luo, J., Gilliland, G. Description: CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY I...

New page

'''Unreleased structure'''

The entry 5i1j is ON HOLD

Authors: Teplyakov, A., Obmolova, G., Malia, T., Luo, J., Gilliland, G.

Description: CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY IGHV5-51/IGKV3-11
[[Category: Unreleased Structures]]
[[Category: Malia, T]]
[[Category: Teplyakov, A]]
[[Category: Gilliland, G]]
[[Category: Obmolova, G]]
[[Category: Luo, J]]