2dtm - Revision history

OCA at 07:55, 30 October 2024

2024-10-30T07:55:47Z

← Older revision		Revision as of 07:55, 30 October 2024
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dt/2dtm_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dt/2dtm_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>

OCA at 08:29, 25 October 2023

2023-10-25T08:29:53Z

← Older revision		Revision as of 08:29, 25 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dtm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DTM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dtm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DTM FirstGlance]. <br>
	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~<div style='overflow: auto; max~~-~~height: 3em;'>[[2dqt\|2dqt]]~~, [[~~2dqu~~\|~~2dqu~~]]~~</div>~~</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]] 2.25Å</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=2dtm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtm OCA], [https://pdbe.org/2dtm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dtm RCSB], [https://www.ebi.ac.uk/pdbsum/2dtm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dtm 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=2dtm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtm OCA], [https://pdbe.org/2dtm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dtm RCSB], [https://www.ebi.ac.uk/pdbsum/2dtm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dtm ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/A2NHM3_MOUSE A2NHM3_MOUSE]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Fujii, I]]		[[Category: Fujii I]]
	[[Category: Ito, N]]		[[Category: Ito N]]
	[[Category: Oda, M]]		[[Category: Oda M]]
	[[Category: Suzuki, K]]		[[Category: Suzuki K]]
	[[Category: Tsumuraya, T]]		[[Category: Tsumuraya T]]
	~~[[Category: Catalytic antibody]]~~
	~~[[Category: Ester hydrolysis]]~~
	~~[[Category: Esterolytic]]~~
	~~[[Category: Fab]]~~
	~~[[Category: Immune system]]~~
	~~[[Category: Immunoglobulin~~]]

OCA at 17:16, 15 December 2021

2021-12-15T17:16:18Z

← Older revision		Revision as of 17:16, 15 December 2021
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	<StructureSection load='2dtm' size='340' side='right'caption='[[2dtm]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='2dtm' size='340' side='right'caption='[[2dtm]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dtm]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DTM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dtm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DTM FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dqt\|2dqt]], [[2dqu\|2dqu]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2dqt\|2dqt]], [[2dqu\|2dqu]]</div></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=2dtm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtm OCA], [~~http~~://pdbe.org/2dtm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dtm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dtm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dtm 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=2dtm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtm OCA], [https://pdbe.org/2dtm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dtm RCSB], [https://www.ebi.ac.uk/pdbsum/2dtm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dtm ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 08:20, 11 March 2020

2020-03-11T08:20:18Z

← Older revision		Revision as of 08:20, 11 March 2020
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	==Thermodynamic and structural analyses of hydrolytic mechanism by catalytic antibodies==		==Thermodynamic and structural analyses of hydrolytic mechanism by catalytic antibodies==
	<StructureSection load='2dtm' size='340' side='right' caption='[[2dtm]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='2dtm' size='340' side='right'caption='[[2dtm]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dtm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DTM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dtm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DTM FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Fujii, I]]		[[Category: Fujii, I]]

OCA at 06:44, 6 June 2018

2018-06-06T06:44:57Z

← Older revision		Revision as of 06:44, 6 June 2018
Line 1:		Line 1:

	==Thermodynamic and structural analyses of hydrolytic mechanism by catalytic antibodies==		==Thermodynamic and structural analyses of hydrolytic mechanism by catalytic antibodies==
	<StructureSection load='2dtm' size='340' side='right' caption='[[2dtm]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='2dtm' size='340' side='right' caption='[[2dtm]], [[Resolution\|resolution]] 2.25Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2dtm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DTM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dtm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DTM FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dqt\|2dqt]], [[2dqu\|2dqu]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dqt\|2dqt]], [[2dqu\|2dqu]]</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=2dtm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtm OCA], [http://pdbe.org/2dtm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dtm RCSB], [http://www.ebi.ac.uk/pdbsum/2dtm 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=2dtm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtm OCA], [http://pdbe.org/2dtm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dtm RCSB], [http://www.ebi.ac.uk/pdbsum/2dtm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dtm ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dt/2dtm_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dt/2dtm_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2dtm ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	==See Also==		==See Also==
	*[[Monoclonal ~~Antibody~~\|Monoclonal ~~Antibody~~]]		*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:12, 11 September 2015

2015-09-11T15:12:38Z

← Older revision		Revision as of 15:12, 11 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[2dtm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DTM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dtm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DTM FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dqt\|2dqt]], [[2dqu\|2dqu]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dqt\|2dqt]], [[2dqu\|2dqu]]</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=2dtm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dtm RCSB], [http://www.ebi.ac.uk/pdbsum/2dtm 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=2dtm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtm OCA], [http://pdbe.org/2dtm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dtm RCSB], [http://www.ebi.ac.uk/pdbsum/2dtm PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	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 2dtm" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 16:26, 15 January 2015

2015-01-15T16:26:52Z

← Older revision		Revision as of 16:26, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dtm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DTM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dtm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DTM FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dqt\|2dqt]], [[2dqu\|2dqu]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dqt\|2dqt]], [[2dqu\|2dqu]]</td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dtm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dtm RCSB], [http://www.ebi.ac.uk/pdbsum/2dtm 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=2dtm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dtm RCSB], [http://www.ebi.ac.uk/pdbsum/2dtm PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Fujii, I.]]		[[Category: Fujii, I]]
	[[Category: Ito, N.]]		[[Category: Ito, N]]
	[[Category: Oda, M.]]		[[Category: Oda, M]]
	[[Category: Suzuki, K.]]		[[Category: Suzuki, K]]
	[[Category: Tsumuraya, T.]]		[[Category: Tsumuraya, T]]
	[[Category: Catalytic antibody]]		[[Category: Catalytic antibody]]
	[[Category: Ester hydrolysis]]		[[Category: Ester hydrolysis]]

OCA at 01:45, 30 September 2014

2014-09-30T01:45:20Z

← Older revision		Revision as of 01:45, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2dtm~~.~~png~~\|~~left~~\|~~200px~~]]		==Thermodynamic and structural analyses of hydrolytic mechanism by catalytic antibodies==
			<StructureSection load='2dtm' size='340' side='right' caption='[[2dtm]], [[Resolution\|resolution]] 2.25Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2dtm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DTM FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dqt\|2dqt]], [[2dqu\|2dqu]]</td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dtm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dtm RCSB], [http://www.ebi.ac.uk/pdbsum/2dtm PDBsum]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dt/2dtm_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Catalytic antibodies 6D9 and 9C10, which were induced by immunization with a haptenic transition-state analog (TSA), catalyze the hydrolysis of a nonbioactive chloramphenicol monoester derivative to generate a bioactive chloramphenicol. These antibodies stabilize the transition state to catalyze the hydrolysis reaction, strictly according to the theoretical relationship: for 6D9, k(cat)/k(uncat)=895 and K(S)/K(TSA)=900, and for 9C10, k(cat)/k(uncat)=56 and K(S)/K(TSA)=60. To elucidate the molecular basis of the antibody-catalyzed reaction, the crystal structure of 6D9 was determined, and the binding thermodynamics of 6D9 and 9C10 with both the substrate and the TSA were analyzed using isothermal titration calorimetry. The crystal structure of the unliganded 6D9 Fab was determined at 2.25 A resolution and compared with that of the TSA-liganded 6D9 Fab reported previously, showing that the TSA is bound into the hydrophobic pocket of the antigen-combining site in an "induced fit" manner, especially at the L1 and H3 CDR loops. Thermodynamic analyses showed that 6D9 binds the substrate of the TSA with a positive DeltaS, differing from general thermodynamic characteristics of antigen-antibody interactions. This positive DeltaS could be due to the hydrophobic interactions between 6D9 and the substrate or the TSA mediated by Trp H100i. The difference in DeltaG between substrate and TSA-binding to 6D9 was larger than that to 9C10, which is in good correlation with the larger k(cat) value of 6D9. Interestingly, the DeltaDeltaG was mainly because of the DeltaDeltaH. The correlation between k(cat) and DeltaDeltaH is suggestive of "enthalpic strain" leading to destabilization of antibody-substrate complexes. Together with X-ray structural analyses, the thermodynamic analyses suggest that upon binding the substrate, the antibody alters the conformation of the ester moiety in the substrate from the planar Z form to a thermodynamically unstable twisted conformation, followed by conversion into the transition state. Enthalpic strain also contributes to the transition-state stabilization by destabilizing the ground state, and its degree is much larger for the more efficient catalytic antibody, 6D9.

	~~{{STRUCTURE_2dtm\| PDB=2dtm \| SCENE= }}~~		Thermodynamic and structural basis for transition-state stabilization in antibody-catalyzed hydrolysis.,Oda M, Ito N, Tsumuraya T, Suzuki K, Sakakura M, Fujii I J Mol Biol. 2007 May 25;369(1):198-209. Epub 2007 Mar 15. PMID:17428500<ref>PMID:17428500</ref>

	~~===Thermodynamic and structural analyses~~ of ~~hydrolytic mechanism by catalytic antibodies===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>

	~~{{ABSTRACT_PUBMED_17428500}}~~		==See Also==
			*[[Monoclonal Antibody\|Monoclonal Antibody]]
	==~~About this Structure~~==		== References ==
	[[~~2dtm]~~] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTM OCA].		<references/>
			__TOC__
	==~~Reference~~==		</StructureSection>
	<~~ref group="xtra">PMID:017428500<~~/~~ref~~><~~ref group="xtra">PMID:009698565</ref><references group="xtra"~~/>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Fujii, I.]]		[[Category: Fujii, I.]]

OCA at 12:29, 23 January 2013

2013-01-23T12:29:22Z

← Older revision		Revision as of 12:29, 23 January 2013
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	[[Image:2dtm.png\|left\|200px]]		[[Image:2dtm.png\|left\|200px]]

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	~~or leave the SCENE parameter empty for the default display.~~
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	{{STRUCTURE_2dtm\| PDB=2dtm \| SCENE= }}		{{STRUCTURE_2dtm\| PDB=2dtm \| SCENE= }}

	===Thermodynamic and structural analyses of hydrolytic mechanism by catalytic antibodies===		===Thermodynamic and structural analyses of hydrolytic mechanism by catalytic antibodies===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_17428500}}, adds the Publication Abstract to the page~~
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	==Reference==		==Reference==
	<ref group="xtra">PMID:~~17428500~~</ref><ref group="xtra">PMID:~~9698565~~</ref><references group="xtra"/>		<ref group="xtra">PMID:017428500</ref><ref group="xtra">PMID:009698565</ref><references group="xtra"/>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Fujii, I.]]		[[Category: Fujii, I.]]

OCA: Protected "2dtm" [edit=sysop:move=sysop]

2011-03-14T21:49:56Z

Protected "2dtm" [edit=sysop:move=sysop]

← Older revision	Revision as of 21:49, 14 March 2011
(No difference)