5icz - Revision history

OCA at 13:46, 30 August 2023

OCA — Wed, 30 Aug 2023 13:46:19 GMT

←Older revision		Revision as of 13:46, 30 August 2023
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	<StructureSection load='5icz' size='340' side='right'caption='[[5icz]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='5icz' size='340' side='right'caption='[[5icz]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5icz]] 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=5ICZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5ICZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5icz]] 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=5ICZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ICZ 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]] 2.55Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">[[4gw1\|4gw1]], [[4hr8\|4hr8]], [[5esq\|5esq]], [[5etu\|5etu]], [[5euk\|5euk]], [[5f88\|5f88]], [[5ff6\|5ff6]], [[5hpm\|5hpm]], [[5hyq\|5hyq]], [[5i2i\|5i2i]], [[5icy\|5icy]], [[5icx\|5icx]], [[5id0\|5id0]], [[5id1\|5id1]]</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~~://proteopedia.org/fgij/fg.htm?mol=5icz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5icz OCA], [~~http~~://pdbe.org/5icz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5icz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5icz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5icz 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=5icz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5icz OCA], [https://pdbe.org/5icz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5icz RCSB], [https://www.ebi.ac.uk/pdbsum/5icz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5icz 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 07:13, 3 June 2020

OCA — Wed, 03 Jun 2020 07:13:32 GMT

←Older revision		Revision as of 07:13, 3 June 2020
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	==Cetuximab Fab in complex with GQFDLSTRRLKG peptide==		==Cetuximab Fab in complex with GQFDLSTRRLKG peptide==
-	<StructureSection load='5icz' size='340' side='right' caption='[[5icz]], [[Resolution\|resolution]] 2.55Å' scene=''>	+	<StructureSection load='5icz' size='340' side='right'caption='[[5icz]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5icz]] 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=5ICZ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ICZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5icz]] 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=5ICZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ICZ 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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gw1\|4gw1]], [[4hr8\|4hr8]], [[5esq\|5esq]], [[5etu\|5etu]], [[5euk\|5euk]], [[5f88\|5f88]], [[5ff6\|5ff6]], [[5hpm\|5hpm]], [[5hyq\|5hyq]], [[5i2i\|5i2i]], [[5icy\|5icy]], [[5icx\|5icx]], [[5id0\|5id0]], [[5id1\|5id1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gw1\|4gw1]], [[4hr8\|4hr8]], [[5esq\|5esq]], [[5etu\|5etu]], [[5euk\|5euk]], [[5f88\|5f88]], [[5ff6\|5ff6]], [[5hpm\|5hpm]], [[5hyq\|5hyq]], [[5i2i\|5i2i]], [[5icy\|5icy]], [[5icx\|5icx]], [[5id0\|5id0]], [[5id1\|5id1]]</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=5icz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5icz OCA], [http://pdbe.org/5icz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5icz RCSB], [http://www.ebi.ac.uk/pdbsum/5icz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5icz 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=5icz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5icz OCA], [http://pdbe.org/5icz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5icz RCSB], [http://www.ebi.ac.uk/pdbsum/5icz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5icz 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: Large Structures]]
	[[Category: Lk3 transgenic mice]]		[[Category: Lk3 transgenic mice]]
	[[Category: Bzymek, K P]]		[[Category: Bzymek, K P]]

OCA at 07:24, 13 December 2017

OCA — Wed, 13 Dec 2017 07:24:03 GMT

←Older revision		Revision as of 07:24, 13 December 2017
Line 3:		Line 3:
	<StructureSection load='5icz' size='340' side='right' caption='[[5icz]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='5icz' size='340' side='right' caption='[[5icz]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5icz]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ICZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ICZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5icz]] 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=5ICZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ICZ 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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gw1\|4gw1]], [[4hr8\|4hr8]], [[5esq\|5esq]], [[5etu\|5etu]], [[5euk\|5euk]], [[5f88\|5f88]], [[5ff6\|5ff6]], [[5hpm\|5hpm]], [[5hyq\|5hyq]], [[5i2i\|5i2i]], [[5icy\|5icy]], [[5icx\|5icx]], [[5id0\|5id0]], [[5id1\|5id1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gw1\|4gw1]], [[4hr8\|4hr8]], [[5esq\|5esq]], [[5etu\|5etu]], [[5euk\|5euk]], [[5f88\|5f88]], [[5ff6\|5ff6]], [[5hpm\|5hpm]], [[5hyq\|5hyq]], [[5i2i\|5i2i]], [[5icy\|5icy]], [[5icx\|5icx]], [[5id0\|5id0]], [[5id1\|5id1]]</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=5icz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5icz OCA], [http://pdbe.org/5icz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5icz RCSB], [http://www.ebi.ac.uk/pdbsum/5icz 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=5icz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5icz OCA], [http://pdbe.org/5icz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5icz RCSB], [http://www.ebi.ac.uk/pdbsum/5icz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5icz ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Recently, a unique binding site for a cyclic 12-residue peptide was discovered within a cavity formed by the light and heavy chains of the cetuximab Fab domain. In order to better understand the interactions that drive this unique complex, a number of variants including the residues within the meditope peptide and the antibody, as well as the cyclization region of the meditope peptide, were created. Here, multiple crystal structures of meditope peptides incorporating different cyclization strategies bound to the central cavity of the cetuximab Fab domain are presented. The affinity of each cyclic derivative for the Fab was determined by surface plasmon resonance and correlated to structural differences. Overall, it was observed that the disulfide bond used to cyclize the peptide favorably packs against a hydrophobic `pocket' and that amidation and acetylation of the original disulfide meditope increased the overall affinity approximately 2.3-fold. Conversely, replacing the terminal cysteines with serines and thus creating a linear peptide reduced the affinity over 50-fold, with much of this difference being reflected in a decrease in the on-rate. Other cyclization methods, including the formation of a lactam, reduced the affinity but not to the extent of the linear peptide. Collectively, the structural and kinetic data presented here indicate that small perturbations introduced by different cyclization strategies can significantly affect the affinity of the meditope-Fab complex.
		+
		+	Cyclization strategies of meditopes: affinity and diffraction studies of meditope-Fab complexes.,Bzymek KP, Ma Y, Avery KA, Horne DA, Williams JC Acta Crystallogr F Struct Biol Commun. 2016 Jun;72(Pt 6):434-42. doi:, 10.1107/S2053230X16007202. Epub 2016 May 23. PMID:27303895<ref>PMID:27303895</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5icz" 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]]

OCA at 22:26, 20 June 2016

OCA — Mon, 20 Jun 2016 22:26:12 GMT

←Older revision		Revision as of 22:26, 20 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5icz ~~is ON HOLD until Paper Publication~~	+	==Cetuximab Fab in complex with GQFDLSTRRLKG peptide==
-		+	<StructureSection load='5icz' size='340' side='right' caption='[[5icz]], [[Resolution\|resolution]] 2.55Å' scene=''>
-	~~Authors~~: ~~Bzymek, K~~.P.~~, Williams, J~~.C.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5icz]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ICZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ICZ FirstGlance]. <br>
-	~~Description~~: ~~Cetuximab Fab in complex with GQFDLSTRRLKG peptide~~	+	</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gw1\|4gw1]], [[4hr8\|4hr8]], [[5esq\|5esq]], [[5etu\|5etu]], [[5euk\|5euk]], [[5f88\|5f88]], [[5ff6\|5ff6]], [[5hpm\|5hpm]], [[5hyq\|5hyq]], [[5i2i\|5i2i]], [[5icy\|5icy]], [[5icx\|5icx]], [[5id0\|5id0]], [[5id1\|5id1]]</td></tr>
-	[[Category: Bzymek, K.P]]	+	<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=5icz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5icz OCA], [http://pdbe.org/5icz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5icz RCSB], [http://www.ebi.ac.uk/pdbsum/5icz PDBsum]</span></td></tr>
-	[[Category: Williams, J.C]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bzymek, K P]]
		+	[[Category: Williams, J C]]
		+	[[Category: Anti-egfr]]
		+	[[Category: Antibody]]
		+	[[Category: Immune system]]

OCA at 02:08, 10 March 2016

OCA — Thu, 10 Mar 2016 02:08:15 GMT

←Older revision		Revision as of 02:08, 10 March 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

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

-	Description: Cetuximab Fab in complex with ~~cyclic beta-alanine-linked meditope~~	+	Description: Cetuximab Fab in complex with GQFDLSTRRLKG peptide
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Bzymek, K.P]]		[[Category: Bzymek, K.P]]
	[[Category: Williams, J.C]]		[[Category: Williams, J.C]]

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

OCA — Wed, 02 Mar 2016 13:45:46 GMT

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

←Older revision

Revision as of 13:45, 2 March 2016

OCA: New page: '''Unreleased structure''' The entry 5icz is ON HOLD Authors: Bzymek, K.P., Williams, J.C. Description: Cetuximab Fab in complex with cyclic beta-alanine-linked meditope [[Category: Un...

OCA — Wed, 02 Mar 2016 13:45:45 GMT

New page: '''Unreleased structure''' The entry 5icz is ON HOLD Authors: Bzymek, K.P., Williams, J.C. Description: Cetuximab Fab in complex with cyclic beta-alanine-linked meditope [[Category: Un...

New page

'''Unreleased structure'''

The entry 5icz is ON HOLD

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

Description: Cetuximab Fab in complex with cyclic beta-alanine-linked meditope
[[Category: Unreleased Structures]]
[[Category: Bzymek, K.P]]
[[Category: Williams, J.C]]