6s2i - Revision history

OCA at 12:33, 24 January 2024

OCA — Wed, 24 Jan 2024 12:33:46 GMT

←Older revision		Revision as of 12:33, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6s2i' size='340' side='right'caption='[[6s2i]], [[Resolution\|resolution]] 2.29Å' scene=''>		<StructureSection load='6s2i' size='340' side='right'caption='[[6s2i]], [[Resolution\|resolution]] 2.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6s2i]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6S2I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6s2i]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6S2I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NGC:3,5-DIDEOXY-5-[(HYDROXYACETYL)AMINO]-D-GLYCERO-ALPHA-D-GALACTO-NON-2-ULOPYRANOSONIC+ACID'>NGC</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]] 2.285Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6ffj\|6ffj]]</div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NGC:3,5-DIDEOXY-5-[(HYDROXYACETYL)AMINO]-D-GLYCERO-ALPHA-D-GALACTO-NON-2-ULOPYRANOSONIC+ACID'>NGC</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=6s2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s2i OCA], [https://pdbe.org/6s2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6s2i RCSB], [https://www.ebi.ac.uk/pdbsum/6s2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6s2i 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=6s2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s2i OCA], [https://pdbe.org/6s2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6s2i RCSB], [https://www.ebi.ac.uk/pdbsum/6s2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6s2i ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 20:
	==See Also==		==See Also==
	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Bjerregaard-Andersen, K]]	+	[[Category: Bjerregaard-Andersen K]]
-	[[Category: Heggelund~~, J E~~]]	+	[[Category: Heggelund JE]]
-	[[Category: Krengel, U]]	+	[[Category: Krengel U]]
-	~~[[Category: Antibody fragment]]~~	+
-	~~[[Category: Antitumor protein]]~~	+
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Ganglioside]]~~	+
-	~~[[Category: Gm3]]~~	+
-	~~[[Category: Immuno therapy]]~~	+
-	~~[[Category: Scfv]]~~	+
-	~~[[Category: Single chain fragment variable~~]]	+

OCA at 07:05, 27 January 2022

OCA — Thu, 27 Jan 2022 07:05:59 GMT

←Older revision		Revision as of 07:05, 27 January 2022
Line 1:		Line 1:

	==Anti-tumor antibody 14F7-derived scFv in complex with NeuGc Gm3==		==Anti-tumor antibody 14F7-derived scFv in complex with NeuGc Gm3==
-	<StructureSection load='6s2i' size='340' side='right'caption='[[6s2i]]' scene=''>	+	<StructureSection load='6s2i' size='340' side='right'caption='[[6s2i]], [[Resolution\|resolution]] 2.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6S2I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6s2i]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6S2I 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=6s2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s2i OCA], [https://pdbe.org/6s2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6s2i RCSB], [https://www.ebi.ac.uk/pdbsum/6s2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6s2i ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NGC:3,5-DIDEOXY-5-[(HYDROXYACETYL)AMINO]-D-GLYCERO-ALPHA-D-GALACTO-NON-2-ULOPYRANOSONIC+ACID'>NGC</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6ffj\|6ffj]]</div></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=6s2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s2i OCA], [https://pdbe.org/6s2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6s2i RCSB], [https://www.ebi.ac.uk/pdbsum/6s2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6s2i ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Tumor-associated glycolipids such as NeuGc GM3 are auspicious molecular targets in antineoplastic therapies and vaccine strategies. 14F7 is a monoclonal IgG1 with high clinical potential in cancer immunotherapy as it displays extraordinary specificity for NeuGc GM3, while it does not recognize the very similar, ubiquitous NeuAc GM3. Here we present the 2.3 A crystal structure of the 14F7 antigen-binding domain (14F7 scFv) in complex with the NeuGc GM3 trisaccharide. Modeling analysis and previous mutagenesis data suggest that 14F7 may also bind to an alternative NeuGc GM3 conformation, not observed in the crystal structure. The most intriguing finding, however, was that a water molecule centrally placed in the complementarity-determining region directly mediates the specificity of 14F7 to NeuGc GM3. This has profound impact on the complexity of engineering in the binding site and provides an excellent example of the importance in understanding the water structure in antibody-antigen interactions.
		+
		+	Key role of a structural water molecule for the specificity of 14F7-An antitumor antibody targeting the NeuGc GM3 ganglioside.,Bjerregaard-Andersen K, Abraha F, Johannesen H, Oscarson S, Moreno E, Krengel U Glycobiology. 2021 Dec 18;31(11):1500-1509. doi: 10.1093/glycob/cwab076. PMID:34735569<ref>PMID:34735569</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6s2i" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bjerregaard-Andersen K]]	+	[[Category: Lk3 transgenic mice]]
-	[[Category: Heggelund JE]]	+	[[Category: Bjerregaard-Andersen, K]]
-	[[Category: Krengel U]]	+	[[Category: Heggelund, J E]]
		+	[[Category: Krengel, U]]
		+	[[Category: Antibody fragment]]
		+	[[Category: Antitumor protein]]
		+	[[Category: Complex]]
		+	[[Category: Ganglioside]]
		+	[[Category: Gm3]]
		+	[[Category: Immuno therapy]]
		+	[[Category: Scfv]]
		+	[[Category: Single chain fragment variable]]

OCA at 11:07, 10 February 2021

OCA — Wed, 10 Feb 2021 11:07:18 GMT

←Older revision		Revision as of 11:07, 10 February 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6s2i is ~~ON HOLD~~	+	==Anti-tumor antibody 14F7-derived scFv in complex with NeuGc Gm3==
-		+	<StructureSection load='6s2i' size='340' side='right'caption='[[6s2i]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6S2I FirstGlance]. <br>
-	~~Description~~:	+	</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=6s2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s2i OCA], [https://pdbe.org/6s2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6s2i RCSB], [https://www.ebi.ac.uk/pdbsum/6s2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6s2i ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Bjerregaard-Andersen K]]
		+	[[Category: Heggelund JE]]
		+	[[Category: Krengel U]]

OCA: Protected "6s2i" [edit=sysop:move=sysop]

OCA — Wed, 26 Jun 2019 05:32:08 GMT

Protected "6s2i" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:32, 26 June 2019

OCA: New page: '''Unreleased structure''' The entry 6s2i is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 26 Jun 2019 05:32:06 GMT

New page: '''Unreleased structure''' The entry 6s2i is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6s2i is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]