5t1l - Revision history

OCA at 12:53, 4 October 2023

OCA — Wed, 04 Oct 2023 12:53:00 GMT

←Older revision		Revision as of 12:53, 4 October 2023
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	<StructureSection load='5t1l' size='340' side='right'caption='[[5t1l]], [[Resolution\|resolution]] 2.48Å' scene=''>		<StructureSection load='5t1l' size='340' side='right'caption='[[5t1l]], [[Resolution\|resolution]] 2.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5t1l]] is a 6 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=5T1L OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5T1L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5t1l]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens], [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T1L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T1L FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=NAG:N~~-~~ACETYL-D-GLUCOSAMINE'>NAG</scene>~~, ~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.48Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=2GX:BETA-PHENYL-L-PHENYLALANINE'>2GX</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2GX:BETA-PHENYL-L-PHENYLALANINE'>2GX</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td><td class="sblockDat">[[4gw1\|4gw1]], [[4iwe\|4iwe]], [[5t1k\|5t1k]], [[5t1m\|5t1m]], [[5th2\|5th2]], [[5etu\|5etu]], [[5euk\|5euk]], [[5f88\|5f88]], [[5ff6\|5ff6]], [[5i2i\|5i2i]], [[5iop\|5iop]], [[5ir1\|5ir1]], [[5itf\|5itf]], [[5iv2\|5iv2]], [[5ivz\|5ivz]]</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=5t1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t1l OCA], [https://pdbe.org/5t1l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5t1l RCSB], [https://www.ebi.ac.uk/pdbsum/5t1l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5t1l 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=5t1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t1l OCA], [~~http~~://pdbe.org/5t1l PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5t1l RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5t1l PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5t1l 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: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: ~~Bzymek, K P~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Williams, J C~~]]	+	[[Category: Bzymek KP]]
-	[[Category: ~~Anti-egfr]]~~	+	[[Category: Williams JC]]
-	~~[[Category: Antibody]]~~	+
-	~~[[Category: Immune system~~]]	+

OCA at 12:27, 25 December 2019

OCA — Wed, 25 Dec 2019 12:27:10 GMT

←Older revision		Revision as of 12:27, 25 December 2019
Line 1:		Line 1:

	==Cetuximab Fab in complex with CQA(Ph)2DLSTRRLKC peptide==		==Cetuximab Fab in complex with CQA(Ph)2DLSTRRLKC peptide==
-	<StructureSection load='5t1l' size='340' side='right' caption='[[5t1l]], [[Resolution\|resolution]] 2.48Å' scene=''>	+	<StructureSection load='5t1l' size='340' side='right'caption='[[5t1l]], [[Resolution\|resolution]] 2.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5t1l]] is a 6 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=5T1L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T1L FirstGlance]. <br>		<table><tr><td colspan='2'>[[5t1l]] is a 6 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=5T1L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T1L FirstGlance]. <br>
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Lk3 transgenic mice]]		[[Category: Lk3 transgenic mice]]
	[[Category: Bzymek, K P]]		[[Category: Bzymek, K P]]

OCA at 07:46, 6 December 2017

OCA — Wed, 06 Dec 2017 07:46:36 GMT

←Older revision		Revision as of 07:46, 6 December 2017
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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=5t1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t1l OCA], [http://pdbe.org/5t1l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t1l RCSB], [http://www.ebi.ac.uk/pdbsum/5t1l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t1l 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=5t1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t1l OCA], [http://pdbe.org/5t1l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t1l RCSB], [http://www.ebi.ac.uk/pdbsum/5t1l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t1l ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Herein, multiple crystal structures of meditope peptide derivatives incorporating natural and unnatural amino acids bound to the cetuximab Fab domain are presented. The affinity of each derivative was determined by surface plasmon resonance and correlated to the atomic structure. Overall, it was observed that the hydrophobic residues in the meditope peptide, Phe3, Leu5 and Leu10, could accommodate a number of moderate substitutions, but these invariably reduced the overall affinity and half-life of the interaction. In one case, the substitution of Phe3 by histidine led to a change in the rotamer conformation, in which the imidazole ring flipped to a solvent-exposed position. Based on this observation, Phe3 was substituted by diphenylalanine and it was found that the phenyl rings in this variant mimic the superposition of the Phe3 and His3 structures, producing a moderate increase, of 1.4-fold, in the half-life of the complex. In addition, it was observed that substitution of Leu5 by tyrosine and glutamate strongly reduced the affinity, whereas the substitution of Leu5 by diphenylalanine moderately reduced the half-life (by approximately fivefold). Finally, it was observed that substitution of Arg8 and Arg9 by citrulline dramatically reduced the overall affinity, presumably owing to lost electrostatic interactions. Taken together, these studies provide insight into the meditope-cetuximab interaction at the atomic level.
		+
		+	Natural and non-natural amino-acid side-chain substitutions: affinity and diffraction studies of meditope-Fab complexes.,Bzymek KP, Avery KA, Ma Y, Horne DA, Williams JC Acta Crystallogr F Struct Biol Commun. 2016 Nov 1;72(Pt 11):820-830. doi:, 10.1107/S2053230X16016149. Epub 2016 Oct 24. PMID:27834791<ref>PMID:27834791</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5t1l" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 14:20, 6 November 2017

OCA — Mon, 06 Nov 2017 14:20:13 GMT

←Older revision		Revision as of 14:20, 6 November 2017
Line 3:		Line 3:
	<StructureSection load='5t1l' size='340' side='right' caption='[[5t1l]], [[Resolution\|resolution]] 2.48Å' scene=''>		<StructureSection load='5t1l' size='340' side='right' caption='[[5t1l]], [[Resolution\|resolution]] 2.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5t1l]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T1L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T1L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5t1l]] is a 6 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=5T1L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T1L FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2GX:BETA-PHENYL-L-PHENYLALANINE'>2GX</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2GX:BETA-PHENYL-L-PHENYLALANINE'>2GX</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Bzymek, K P]]		[[Category: Bzymek, K P]]
	[[Category: Williams, J C]]		[[Category: Williams, J C]]

OCA at 20:09, 9 December 2016

OCA — Fri, 09 Dec 2016 20:09:51 GMT

←Older revision		Revision as of 20:09, 9 December 2016
Line 6:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2GX:BETA-PHENYL-L-PHENYLALANINE'>2GX</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2GX:BETA-PHENYL-L-PHENYLALANINE'>2GX</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gw1\|4gw1]], [[5t1k\|5t1k]], [[5t1m\|5t1m]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gw1\|4gw1]], [[4iwe\|4iwe]], [[5t1k\|5t1k]], [[5t1m\|5t1m]], [[5th2\|5th2]], [[5etu\|5etu]], [[5euk\|5euk]], [[5f88\|5f88]], [[5ff6\|5ff6]], [[5i2i\|5i2i]], [[5iop\|5iop]], [[5ir1\|5ir1]], [[5itf\|5itf]], [[5iv2\|5iv2]], [[5ivz\|5ivz]]</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=5t1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t1l OCA], [http://pdbe.org/5t1l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t1l RCSB], [http://www.ebi.ac.uk/pdbsum/5t1l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t1l 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=5t1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t1l OCA], [http://pdbe.org/5t1l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t1l RCSB], [http://www.ebi.ac.uk/pdbsum/5t1l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t1l ProSAT]</span></td></tr>
	</table>		</table>

OCA at 18:50, 26 October 2016

OCA — Wed, 26 Oct 2016 18:50:18 GMT

←Older revision		Revision as of 18:50, 26 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5t1l is ON HOLD until Paper Publication~~	+	==Cetuximab Fab in complex with CQA(Ph)2DLSTRRLKC peptide==
-		+	<StructureSection load='5t1l' size='340' side='right' caption='[[5t1l]], [[Resolution\|resolution]] 2.48Å' scene=''>
-	~~Authors: Bzymek, K.P., Williams, J.C.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5t1l]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T1L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T1L FirstGlance]. <br>
-	~~Description:~~ Cetuximab Fab in complex with CQA(Ph)2DLSTRRLKC peptide	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2GX:BETA-PHENYL-L-PHENYLALANINE'>2GX</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
-	[[Category: Bzymek, K.P]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gw1\|4gw1]], [[5t1k\|5t1k]], [[5t1m\|5t1m]]</td></tr>
-	[[Category: Williams, J.C]]	+	<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=5t1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t1l OCA], [http://pdbe.org/5t1l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t1l RCSB], [http://www.ebi.ac.uk/pdbsum/5t1l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t1l ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bzymek, K P]]
		+	[[Category: Williams, J C]]
		+	[[Category: Anti-egfr]]
		+	[[Category: Antibody]]
		+	[[Category: Immune system]]

OCA: Protected "5t1l" [edit=sysop:move=sysop]

OCA — Fri, 09 Sep 2016 15:33:11 GMT

Protected "5t1l" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:33, 9 September 2016

OCA: New page: '''Unreleased structure''' The entry 5t1l is ON HOLD until Paper Publication Authors: Bzymek, K.P., Williams, J.C. Description: Cetuximab Fab in complex with CQA(Ph)2DLSTRRLKC peptide ...

OCA — Fri, 09 Sep 2016 15:33:10 GMT

New page: '''Unreleased structure''' The entry 5t1l is ON HOLD until Paper Publication Authors: Bzymek, K.P., Williams, J.C. Description: Cetuximab Fab in complex with CQA(Ph)2DLSTRRLKC peptide ...

New page

'''Unreleased structure'''

The entry 5t1l is ON HOLD until Paper Publication

Authors: Bzymek, K.P., Williams, J.C.

Description: Cetuximab Fab in complex with CQA(Ph)2DLSTRRLKC peptide
[[Category: Unreleased Structures]]
[[Category: Bzymek, K.P]]
[[Category: Williams, J.C]]