5adp - Revision history

OCA at 11:07, 10 January 2024

OCA — Wed, 10 Jan 2024 11:07:48 GMT

←Older revision		Revision as of 11:07, 10 January 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5adp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ADP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ADP FirstGlance]. <br>		<table><tr><td colspan='2'>[[5adp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ADP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ADP 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=5adp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5adp OCA], [https://pdbe.org/5adp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5adp RCSB], [https://www.ebi.ac.uk/pdbsum/5adp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5adp ProSAT]</span></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]] 2.13Å</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=5adp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5adp OCA], [https://pdbe.org/5adp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5adp RCSB], [https://www.ebi.ac.uk/pdbsum/5adp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5adp ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 04:52, 25 May 2023

OCA — Thu, 25 May 2023 04:52:40 GMT

←Older revision		Revision as of 04:52, 25 May 2023
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	<StructureSection load='5adp' size='340' side='right'caption='[[5adp]], [[Resolution\|resolution]] 2.13Å' scene=''>		<StructureSection load='5adp' size='340' side='right'caption='[[5adp]], [[Resolution\|resolution]] 2.13Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5adp]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ADP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ADP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5adp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ADP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ADP FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ado\|5ado]]</td></tr>~~	+	</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=5adp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5adp OCA], [https://pdbe.org/5adp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5adp RCSB], [https://www.ebi.ac.uk/pdbsum/5adp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5adp 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=5adp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5adp OCA], [~~http~~://pdbe.org/5adp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5adp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5adp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5adp ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Belogurov~~, A A~~]]	+	[[Category: Belogurov AA]]
-	[[Category: Blackburn~~, G M~~]]	+	[[Category: Blackburn GM]]
-	[[Category: Chatziefthimiou~~, S D~~]]	+	[[Category: Chatziefthimiou SD]]
-	[[Category: Gabibov~~, A A~~]]	+	[[Category: Gabibov AA]]
-	[[Category: Golovin~~, A V~~]]	+	[[Category: Golovin AV]]
-	[[Category: Lerner, R]]	+	[[Category: Lerner R]]
-	[[Category: Peng, Y]]	+	[[Category: Peng Y]]
-	[[Category: Ponomarenko~~, N A~~]]	+	[[Category: Ponomarenko NA]]
-	[[Category: Smirnov~~, I V~~]]	+	[[Category: Smirnov IV]]
-	[[Category: Stepanova~~, A V~~]]	+	[[Category: Stepanova AV]]
-	[[Category: Wilmanns, M]]	+	[[Category: Wilmanns M]]
-	[[Category: Zolotareva~~, O I]]~~	+	[[Category: Zolotareva OI]]
-	~~[[Category: Antibody]]~~	+
-	~~[[Category: Enzyme reprogramming]]~~	+
-	~~[[Category: Ig superfamily]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: In silico antibody maturation~~]]	+

OCA at 07:21, 3 July 2019

OCA — Wed, 03 Jul 2019 07:21:57 GMT

←Older revision		Revision as of 07:21, 3 July 2019
Line 1:		Line 1:

	==Crystal structure of the A.17 antibody FAB fragment - Light chain S35R mutant==		==Crystal structure of the A.17 antibody FAB fragment - Light chain S35R mutant==
-	<StructureSection load='5adp' size='340' side='right' caption='[[5adp]], [[Resolution\|resolution]] 2.13Å' scene=''>	+	<StructureSection load='5adp' size='340' side='right'caption='[[5adp]], [[Resolution\|resolution]] 2.13Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5adp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ADP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ADP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5adp]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ADP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ADP FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ado\|5ado]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ado\|5ado]]</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=5adp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5adp OCA], [http://pdbe.org/5adp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5adp RCSB], [http://www.ebi.ac.uk/pdbsum/5adp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5adp 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=5adp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5adp OCA], [http://pdbe.org/5adp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5adp RCSB], [http://www.ebi.ac.uk/pdbsum/5adp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5adp ProSAT]</span></td></tr>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Belogurov, A A]]		[[Category: Belogurov, A A]]
	[[Category: Blackburn, G M]]		[[Category: Blackburn, G M]]

OCA at 19:43, 9 December 2016

OCA — Fri, 09 Dec 2016 19:43:36 GMT

←Older revision		Revision as of 19:43, 9 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5adp is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of the A.17 antibody FAB fragment - Light chain S35R mutant==
		+	<StructureSection load='5adp' size='340' side='right' caption='[[5adp]], [[Resolution\|resolution]] 2.13Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5adp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ADP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ADP FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ado\|5ado]]</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=5adp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5adp OCA], [http://pdbe.org/5adp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5adp RCSB], [http://www.ebi.ac.uk/pdbsum/5adp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5adp ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In vitro selection of antibodies from large repertoires of immunoglobulin (Ig) combining sites using combinatorial libraries is a powerful tool, with great potential for generating in vivo scavengers for toxins. However, addition of a maturation function is necessary to enable these selected antibodies to more closely mimic the full mammalian immune response. We approached this goal using quantum mechanics/molecular mechanics (QM/MM) calculations to achieve maturation in silico. We preselected A17, an Ig template, from a naive library for its ability to disarm a toxic pesticide related to organophosphorus nerve agents. Virtual screening of 167,538 robotically generated mutants identified an optimum single point mutation, which experimentally boosted wild-type Ig scavenger performance by 170-fold. We validated the QM/MM predictions via kinetic analysis and crystal structures of mutant apo-A17 and covalently modified Ig, thereby identifying the displacement of one water molecule by an arginine as delivering this catalysis.

-	~~Authors: Chatziefthimiou, S.D~~., Smirnov~~, I.V.~~, Golovin, ~~A.V.~~, Stepanova~~, A.V.~~, Peng, Y., Zolotareva~~, O.I.~~, Belogurov, ~~A.A.~~, Ponomarenko, ~~N.A.~~, Blackburn~~, G.M.~~, Gabibov, A.A.~~, Lerner, R., Wilmanns, M~~.	+	Robotic QM/MM-driven maturation of antibody combining sites.,Smirnov IV, Golovin AV, Chatziefthimiou SD, Stepanova AV, Peng Y, Zolotareva OI, Belogurov AA Jr, Kurkova IN, Ponomarenko NA, Wilmanns M, Blackburn GM, Gabibov AG, Lerner RA Sci Adv. 2016 Oct 19;2(10):e1501695. eCollection 2016 Oct. PMID:27774510<ref>PMID:27774510</ref>

-	~~Description: Crystal structure~~ of the A.~~17 antibody FAB fragment -Light chain S35R mutant~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	~~[[Category: Ponomarenko, N.A]]~~	+	<div class="pdbe-citations 5adp" style="background-color:#fffaf0;"></div>
-	[[Category: Belogurov, A.A]]	+	== References ==
-	~~[[Category: Zolotareva, O.I~~]]	+	<references/>
-	[[Category: Blackburn, G.M]]	+	__TOC__
-	~~[[Category: Gabibov, A.A]]~~	+	</StructureSection>
-	~~[[Category: Wilmanns, M]]~~	+	[[Category: Belogurov, A A]]
-	~~[[Category: Stepanova, A.V~~]]	+	[[Category: Blackburn, G M]]
-	[[Category: Chatziefthimiou, S.D]]	+	[[Category: Chatziefthimiou, S D]]
-	[[Category: ~~Golovin~~, A.V]]	+	[[Category: Gabibov, A A]]
-	[[Category: ~~Smirnov~~, I.V]]	+	[[Category: Golovin, A V]]
	[[Category: Lerner, R]]		[[Category: Lerner, R]]
	[[Category: Peng, Y]]		[[Category: Peng, Y]]
		+	[[Category: Ponomarenko, N A]]
		+	[[Category: Smirnov, I V]]
		+	[[Category: Stepanova, A V]]
		+	[[Category: Wilmanns, M]]
		+	[[Category: Zolotareva, O I]]
		+	[[Category: Antibody]]
		+	[[Category: Enzyme reprogramming]]
		+	[[Category: Ig superfamily]]
		+	[[Category: Immune system]]
		+	[[Category: In silico antibody maturation]]

OCA at 09:45, 16 December 2015

OCA — Wed, 16 Dec 2015 09:45:49 GMT

←Older revision		Revision as of 09:45, 16 December 2015
Line 7:		Line 7:
	Description: Crystal structure of the A.17 antibody FAB fragment -Light chain S35R mutant		Description: Crystal structure of the A.17 antibody FAB fragment -Light chain S35R mutant
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Ponomarenko, N.A]]
		+	[[Category: Belogurov, A.A]]
	[[Category: Zolotareva, O.I]]		[[Category: Zolotareva, O.I]]
	[[Category: Blackburn, G.M]]		[[Category: Blackburn, G.M]]
	[[Category: Gabibov, A.A]]		[[Category: Gabibov, A.A]]
	[[Category: Wilmanns, M]]		[[Category: Wilmanns, M]]
		+	[[Category: Stepanova, A.V]]
	[[Category: Chatziefthimiou, S.D]]		[[Category: Chatziefthimiou, S.D]]
	[[Category: Golovin, A.V]]		[[Category: Golovin, A.V]]
	[[Category: Smirnov, I.V]]		[[Category: Smirnov, I.V]]
	[[Category: Lerner, R]]		[[Category: Lerner, R]]
-	[[Category: Ponomarenko, N.A]]
-	[[Category: Belogurov, A.A]]
-	[[Category: Stepanova, A.V]]
	[[Category: Peng, Y]]		[[Category: Peng, Y]]

OCA at 00:28, 1 December 2015

OCA — Tue, 01 Dec 2015 00:28:44 GMT

←Older revision		Revision as of 00:28, 1 December 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Chatziefthimiou, S.D., Smirnov, I.V., Golovin, A.V., Stepanova, A.V., Peng, Y., Zolotareva, O.I., Belogurov, A.A., Ponomarenko, N.A., Blackburn, G.M., Gabibov, A.A., Lerner, R., Wilmanns, M.		Authors: Chatziefthimiou, S.D., Smirnov, I.V., Golovin, A.V., Stepanova, A.V., Peng, Y., Zolotareva, O.I., Belogurov, A.A., Ponomarenko, N.A., Blackburn, G.M., Gabibov, A.A., Lerner, R., Wilmanns, M.

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

OCA — Wed, 02 Sep 2015 09:48:17 GMT

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

←Older revision

Revision as of 09:48, 2 September 2015

OCA: New page: '''Unreleased structure''' The entry 5adp is ON HOLD Authors: Chatziefthimiou, S.D., Smirnov, I.V., Golovin, A.V., Stepanova, A.V., Peng, Y., Zolotareva, O.I., Belogurov, A.A., Ponomare...

OCA — Wed, 02 Sep 2015 09:48:15 GMT

New page: '''Unreleased structure''' The entry 5adp is ON HOLD Authors: Chatziefthimiou, S.D., Smirnov, I.V., Golovin, A.V., Stepanova, A.V., Peng, Y., Zolotareva, O.I., Belogurov, A.A., Ponomare...

New page

'''Unreleased structure'''

The entry 5adp is ON HOLD

Authors: Chatziefthimiou, S.D., Smirnov, I.V., Golovin, A.V., Stepanova, A.V., Peng, Y., Zolotareva, O.I., Belogurov, A.A., Ponomarenko, N.A., Blackburn, G.M., Gabibov, A.A., Lerner, R., Wilmanns, M.

Description: Crystal structure of the A.17 antibody FAB fragment -Light chain S35R mutant
[[Category: Unreleased Structures]]
[[Category: Zolotareva, O.I]]
[[Category: Blackburn, G.M]]
[[Category: Gabibov, A.A]]
[[Category: Wilmanns, M]]
[[Category: Chatziefthimiou, S.D]]
[[Category: Golovin, A.V]]
[[Category: Smirnov, I.V]]
[[Category: Lerner, R]]
[[Category: Ponomarenko, N.A]]
[[Category: Belogurov, A.A]]
[[Category: Stepanova, A.V]]
[[Category: Peng, Y]]