4tuk - Revision history

OCA at 12:24, 20 December 2023

OCA — Wed, 20 Dec 2023 12:24:45 GMT

←Older revision		Revision as of 12:24, 20 December 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4tuk]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Phage_#D Phage #D]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TUK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TUK FirstGlance]. <br>		<table><tr><td colspan='2'>[[4tuk]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Phage_#D Phage #D]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TUK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TUK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 1.6Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=4tuk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tuk OCA], [https://pdbe.org/4tuk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4tuk RCSB], [https://www.ebi.ac.uk/pdbsum/4tuk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4tuk 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=4tuk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tuk OCA], [https://pdbe.org/4tuk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4tuk RCSB], [https://www.ebi.ac.uk/pdbsum/4tuk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4tuk ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:56, 15 March 2023

OCA — Wed, 15 Mar 2023 10:56:16 GMT

←Older revision		Revision as of 10:56, 15 March 2023
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	<StructureSection load='4tuk' size='340' side='right'caption='[[4tuk]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='4tuk' size='340' side='right'caption='[[4tuk]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4tuk]] is a 3 chain structure with sequence from [~~http~~://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=4TUK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4TUK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4tuk]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Phage_#D Phage #D]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TUK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TUK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tul\|4tul]], [[4tuo\|4tuo]]~~</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=4tuk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tuk OCA], [https://pdbe.org/4tuk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4tuk RCSB], [https://www.ebi.ac.uk/pdbsum/4tuk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4tuk 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=4tuk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tuk OCA], [~~http~~://pdbe.org/4tuk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4tuk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4tuk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4tuk ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Dubin, G]]	+	[[Category: Phage #D]]
-	[[Category: Golik, P]]	+	[[Category: Dubin G]]
-	[[Category: Grudnik, P]]	+	[[Category: Golik P]]
-	[[Category: Horwacik, I]]	+	[[Category: Grudnik P]]
-	[[Category: Rokita, H]]	+	[[Category: Horwacik I]]
-	[[Category: Zdzalik, M]]	+	[[Category: Rokita H]]
-	~~[[Category: Immune system]]~~	+	[[Category: Zdzalik M]]
-	~~[[Category: Neuroblastoma~~]]	+

OCA at 08:03, 19 February 2020

OCA — Wed, 19 Feb 2020 08:03:37 GMT

←Older revision		Revision as of 08:03, 19 February 2020
Line 1:		Line 1:

	==Crystal structure of monoclonal antibody against neuroblastoma associated antigen.==		==Crystal structure of monoclonal antibody against neuroblastoma associated antigen.==
-	<StructureSection load='4tuk' size='340' side='right' caption='[[4tuk]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='4tuk' size='340' side='right'caption='[[4tuk]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4tuk]] is a 3 chain structure with sequence from [http://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=4TUK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TUK FirstGlance]. <br>		<table><tr><td colspan='2'>[[4tuk]] is a 3 chain structure with sequence from [http://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=4TUK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TUK FirstGlance]. <br>
Line 24:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Lk3 transgenic mice]]		[[Category: Lk3 transgenic mice]]
	[[Category: Dubin, G]]		[[Category: Dubin, G]]

OCA at 05:56, 8 March 2018

OCA — Thu, 08 Mar 2018 05:56:24 GMT

←Older revision		Revision as of 05:56, 8 March 2018
Line 1:		Line 1:
		+
	==Crystal structure of monoclonal antibody against neuroblastoma associated antigen.==		==Crystal structure of monoclonal antibody against neuroblastoma associated antigen.==
	<StructureSection load='4tuk' size='340' side='right' caption='[[4tuk]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='4tuk' size='340' side='right' caption='[[4tuk]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4tuk]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TUK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TUK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4tuk]] is a 3 chain structure with sequence from [http://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=4TUK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TUK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tul\|4tul]], [[4tuo\|4tuo]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tul\|4tul]], [[4tuo\|4tuo]]</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=4tuk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tuk OCA], [http://pdbe.org/4tuk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4tuk RCSB], [http://www.ebi.ac.uk/pdbsum/4tuk 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=4tuk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tuk OCA], [http://pdbe.org/4tuk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4tuk RCSB], [http://www.ebi.ac.uk/pdbsum/4tuk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4tuk ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 4tuk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4tuk" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Dubin, G]]		[[Category: Dubin, G]]
	[[Category: Golik, P]]		[[Category: Golik, P]]

OCA at 21:46, 15 October 2015

OCA — Thu, 15 Oct 2015 21:46:29 GMT

←Older revision		Revision as of 21:46, 15 October 2015
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tul\|4tul]], [[4tuo\|4tuo]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tul\|4tul]], [[4tuo\|4tuo]]</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=4tuk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tuk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4tuk RCSB], [http://www.ebi.ac.uk/pdbsum/4tuk 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=4tuk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tuk OCA], [http://pdbe.org/4tuk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4tuk RCSB], [http://www.ebi.ac.uk/pdbsum/4tuk PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 15:
	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 4tuk" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:26, 29 July 2015

OCA — Wed, 29 Jul 2015 08:26:29 GMT

←Older revision		Revision as of 08:26, 29 July 2015
Line 7:		Line 7:
	<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=4tuk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tuk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4tuk RCSB], [http://www.ebi.ac.uk/pdbsum/4tuk 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=4tuk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tuk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4tuk RCSB], [http://www.ebi.ac.uk/pdbsum/4tuk PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Monoclonal antibodies targeting GD2 ganglioside (GD2) have recently been approved for the treatment of high risk neuroblastoma and are extensively evaluated in clinics in other indications. This study illustrates how a therapeutic antibody distinguishes between different types of gangliosides present on normal and cancer cells and informs how synthetic peptides can imitate ganglioside in its binding to the antibody. Using high resolution crystal structures we demonstrate that the ganglioside recognition by a model antibody (14G2a) is based primarily on an extended network of direct and water molecule mediated hydrogen bonds. Comparison of the GD2-Fab structure with that of a ligand free antibody reveals an induced fit mechanism of ligand binding. These conclusions are validated by directed mutagenesis and allowed structure guided generation of antibody variant with improved affinity towards GD2. Contrary to the carbohydrate, both evaluated mimetic peptides utilize a key and lock interaction mechanism complementing the surface of the antibody binding groove exactly as found in the empty structure. The interaction of both peptides with the Fab relies considerably on hydrophobic contacts however, the detailed connections differ significantly between the peptides. As such, the evaluated peptide carbohydrate mimicry is defined primarily in a functional and not in structural manner.
		+
		+	Structural basis of GD2 ganglioside and mimetic peptide recognition by 14G2a antibody.,Horwacik I, Golik P, Grudnik P, Kolinski M, Zdzalik M, Rokita H, Dubin G Mol Cell Proteomics. 2015 Jul 15. pii: mcp.M115.052720. PMID:26179345<ref>PMID:26179345</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 13:32, 15 July 2015

OCA — Wed, 15 Jul 2015 13:32:10 GMT

←Older revision		Revision as of 13:32, 15 July 2015
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal structure of monoclonal antibody against neuroblastoma associated antigen.==
-		+	<StructureSection load='4tuk' size='340' side='right' caption='[[4tuk]], [[Resolution\|resolution]] 1.60Å' scene=''>
-	~~The entry~~ 4tuk is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4tuk]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TUK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TUK FirstGlance]. <br>
-	~~Authors~~: ~~Golik, P~~.~~, Grudnik, P~~.~~, Dubin, G~~.~~, Horwacik, I~~.~~, Zdzalik, M~~.~~, Rokita, H~~.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tul\|4tul]], [[4tuo\|4tuo]]</td></tr>
-	~~Description: Crystal structure of monoclonal antibody against neuroblastoma associated antigen~~.	+	<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=4tuk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tuk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4tuk RCSB], [http://www.ebi.ac.uk/pdbsum/4tuk PDBsum]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Grudnik~~, P]]	+	__TOC__
-	[[~~Category~~: ~~Zdzalik~~, M]]	+	</StructureSection>
	[[Category: Dubin, G]]		[[Category: Dubin, G]]
-	[[Category: Horwacik, I]]
	[[Category: Golik, P]]		[[Category: Golik, P]]
		+	[[Category: Grudnik, P]]
		+	[[Category: Horwacik, I]]
	[[Category: Rokita, H]]		[[Category: Rokita, H]]
		+	[[Category: Zdzalik, M]]
		+	[[Category: Immune system]]
		+	[[Category: Neuroblastoma]]

OCA at 17:52, 24 December 2014

OCA — Wed, 24 Dec 2014 17:52:58 GMT

←Older revision		Revision as of 17:52, 24 December 2014
Line 6:		Line 6:

	Description: Crystal structure of monoclonal antibody against neuroblastoma associated antigen.		Description: Crystal structure of monoclonal antibody against neuroblastoma associated antigen.
		+	[[Category: Unreleased Structures]]
		+	[[Category: Grudnik, P]]
		+	[[Category: Zdzalik, M]]
		+	[[Category: Dubin, G]]
		+	[[Category: Horwacik, I]]
		+	[[Category: Golik, P]]
		+	[[Category: Rokita, H]]

OCA at 06:57, 9 July 2014

OCA — Wed, 09 Jul 2014 06:57:45 GMT

←Older revision		Revision as of 06:57, 9 July 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Golik, P., Grudnik, P., Dubin, G., Horwacik, I., Zdzalik, M., Rokita, H.		Authors: Golik, P., Grudnik, P., Dubin, G., Horwacik, I., Zdzalik, M., Rokita, H.

	Description: Crystal structure of monoclonal antibody against neuroblastoma associated antigen.		Description: Crystal structure of monoclonal antibody against neuroblastoma associated antigen.

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

OCA — Wed, 02 Jul 2014 07:34:54 GMT

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

←Older revision

Revision as of 07:34, 2 July 2014