5i2i - Revision history

OCA at 08:20, 23 August 2023

OCA — Wed, 23 Aug 2023 08:20:58 GMT

←Older revision		Revision as of 08:20, 23 August 2023
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	<StructureSection load='5i2i' size='340' side='right'caption='[[5i2i]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='5i2i' size='340' side='right'caption='[[5i2i]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i2i]] 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=5I2I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5I2I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i2i]] 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=5I2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5I2I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 2.551Å</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=5i2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i2i OCA], [~~http~~://pdbe.org/5i2i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5i2i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5i2i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5i2i ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=5i2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i2i OCA], [https://pdbe.org/5i2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5i2i RCSB], [https://www.ebi.ac.uk/pdbsum/5i2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5i2i 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: ~~Antibody]]~~	+	[[Category: Williams JC]]
-	~~[[Category: Immune system~~]]	+

OCA at 08:42, 27 May 2020

OCA — Wed, 27 May 2020 08:42:44 GMT

←Older revision		Revision as of 08:42, 27 May 2020
Line 1:		Line 1:

	==Structure of cetuximab Fab with cyclic F3Q variant of the meditope==		==Structure of cetuximab Fab with cyclic F3Q variant of the meditope==
-	<StructureSection load='5i2i' size='340' side='right' caption='[[5i2i]], [[Resolution\|resolution]] 2.55Å' scene=''>	+	<StructureSection load='5i2i' size='340' side='right'caption='[[5i2i]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i2i]] 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=5I2I OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5I2I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i2i]] 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=5I2I OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5I2I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=5i2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i2i OCA], [http://pdbe.org/5i2i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i2i RCSB], [http://www.ebi.ac.uk/pdbsum/5i2i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i2i 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=5i2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i2i OCA], [http://pdbe.org/5i2i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i2i RCSB], [http://www.ebi.ac.uk/pdbsum/5i2i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i2i ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	__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 07:23, 13 December 2017

OCA — Wed, 13 Dec 2017 07:23:47 GMT

←Older revision		Revision as of 07:23, 13 December 2017
Line 3:		Line 3:
	<StructureSection load='5i2i' size='340' side='right' caption='[[5i2i]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='5i2i' size='340' side='right' caption='[[5i2i]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i2i]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I2I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I2I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i2i]] 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=5I2I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I2I FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=PO4:PHOSPHATE+ION'>PO4</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=5i2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i2i OCA], [http://pdbe.org/5i2i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i2i RCSB], [http://www.ebi.ac.uk/pdbsum/5i2i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i2i 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=5i2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i2i OCA], [http://pdbe.org/5i2i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i2i RCSB], [http://www.ebi.ac.uk/pdbsum/5i2i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i2i 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 5i2i" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Bzymek, K P]]		[[Category: Bzymek, K P]]
	[[Category: Williams, J C]]		[[Category: Williams, J C]]
	[[Category: Antibody]]		[[Category: Antibody]]
	[[Category: Immune system]]		[[Category: Immune system]]

OCA at 18:43, 26 October 2016

OCA — Wed, 26 Oct 2016 18:43:57 GMT

←Older revision		Revision as of 18:43, 26 October 2016
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-	'''Unreleased structure'''

-	~~The entry 5i2i is ON HOLD until Feb 08 2018~~	+	==Structure of cetuximab Fab with cyclic F3Q variant of the meditope==
-		+	<StructureSection load='5i2i' size='340' side='right' caption='[[5i2i]], [[Resolution\|resolution]] 2.55Å' scene=''>
-	~~Authors: Bzymek, K.P., Williams, J.C.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5i2i]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I2I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I2I FirstGlance]. <br>
-	~~Description:~~ Structure of cetuximab Fab with cyclic F3Q variant of the meditope	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=5i2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i2i OCA], [http://pdbe.org/5i2i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i2i RCSB], [http://www.ebi.ac.uk/pdbsum/5i2i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i2i ProSAT]</span></td></tr>
-	[[Category: Bzymek, K.P]]	+	</table>
-	[[Category: Williams, J.C]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Bzymek, K P]]
		+	[[Category: Williams, J C]]
		+	[[Category: Antibody]]
		+	[[Category: Immune system]]

OCA at 13:17, 2 March 2016

OCA — Wed, 02 Mar 2016 13:17:37 GMT

←Older revision		Revision as of 13:17, 2 March 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5i2i is ON HOLD	+	The entry 5i2i is ON HOLD until Feb 08 2018

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

OCA: Protected "5i2i" [edit=sysop:move=sysop]

OCA — Sun, 21 Feb 2016 01:28:50 GMT

Protected "5i2i" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:28, 21 February 2016

OCA: New page: '''Unreleased structure''' The entry 5i2i is ON HOLD Authors: Bzymek, K.P., Williams, J.C. Description: Structure of cetuximab Fab with cyclic F3Q variant of the meditope [[Category: U...

OCA — Sun, 21 Feb 2016 01:28:49 GMT

New page: '''Unreleased structure''' The entry 5i2i is ON HOLD Authors: Bzymek, K.P., Williams, J.C. Description: Structure of cetuximab Fab with cyclic F3Q variant of the meditope [[Category: U...

New page

'''Unreleased structure'''

The entry 5i2i is ON HOLD

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

Description: Structure of cetuximab Fab with cyclic F3Q variant of the meditope
[[Category: Unreleased Structures]]
[[Category: Bzymek, K.P]]
[[Category: Williams, J.C]]