2vmf - Revision history

OCA at 15:25, 13 December 2023

2023-12-13T15:25:09Z

← Older revision		Revision as of 15:25, 13 December 2023
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	<StructureSection load='2vmf' size='340' side='right'caption='[[2vmf]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2vmf' size='340' side='right'caption='[[2vmf]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2vmf]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bactn Bactn~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VMF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2VMF FirstGlance]. <br>		<table><tr><td colspan='2'>[[2vmf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron_VPI-5482 Bacteroides thetaiotaomicron VPI-5482]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VMF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VMF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MVL:(5R,6R,7S,8R)-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL'>MVL</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]] 2.1Å</td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2vqt\|2vqt]], [[2vot\|2vot]], [[2vl4\|2vl4]], [[2vqu\|2vqu]], [[2vo5\|2vo5]], [[2je8\|2je8]], [[2vjx\|2vjx]]</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MVL:(5R,6R,7S,8R)-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL'>MVL</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-mannosidase Beta-mannosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.25 3.2.1.25] </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=2vmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vmf OCA], [https://pdbe.org/2vmf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vmf RCSB], [https://www.ebi.ac.uk/pdbsum/2vmf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vmf 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=2vmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vmf OCA], [~~http~~://pdbe.org/2vmf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2vmf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2vmf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2vmf ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/Q8AAK6_BACTN Q8AAK6_BACTN]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Bactn]]~~		[[Category: Bacteroides thetaiotaomicron VPI-5482]]
	~~[[Category: Beta~~-~~mannosidase~~]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bleriot, Y]]		[[Category: Bleriot Y]]
	[[Category: Davies~~, G J~~]]		[[Category: Davies GJ]]
	[[Category: Dumon, C]]		[[Category: Dumon C]]
	[[Category: Gilbert~~, H J~~]]		[[Category: Gilbert HJ]]
	[[Category: Gratien, J]]		[[Category: Gratien J]]
	[[Category: Heck~~, M P~~]]		[[Category: Heck MP]]
	[[Category: Moreland, C]]		[[Category: Moreland C]]
	[[Category: Offen~~, W A~~]]		[[Category: Offen WA]]
	[[Category: Smith~~, N L~~]]		[[Category: Smith NL]]
	[[Category: Stick~~, R V~~]]		[[Category: Stick RV]]
	[[Category: Tailford~~, L E~~]]		[[Category: Tailford LE]]
	[[Category: Vasella, A]]		[[Category: Vasella A]]
	~~[[Category: Glycoside hydrolase]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Linear free energy relationship]]~~
	~~[[Category: Mannosidase]]~~
	~~[[Category: Transition state mimic~~]]

OCA at 06:54, 19 August 2020

2020-08-19T06:54:56Z

← Older revision		Revision as of 06:54, 19 August 2020
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	==Structural and biochemical evidence for a boat-like transition state in beta-mannosidases==		==Structural and biochemical evidence for a boat-like transition state in beta-mannosidases==
	<StructureSection load='2vmf' size='340' side='right' caption='[[2vmf]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2vmf' size='340' side='right'caption='[[2vmf]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2vmf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bactn Bactn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VMF OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2VMF FirstGlance]. <br>		<table><tr><td colspan='2'>[[2vmf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bactn Bactn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VMF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2VMF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MVL:(5R,6R,7S,8R)-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL'>MVL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MVL:(5R,6R,7S,8R)-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL'>MVL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2vqt\|2vqt]], [[2vot\|2vot]], [[2vl4\|2vl4]], [[2vqu\|2vqu]], [[2vo5\|2vo5]], [[2je8\|2je8]], [[2vjx\|2vjx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2vqt\|2vqt]], [[2vot\|2vot]], [[2vl4\|2vl4]], [[2vqu\|2vqu]], [[2vo5\|2vo5]], [[2je8\|2je8]], [[2vjx\|2vjx]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-mannosidase Beta-mannosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.25 3.2.1.25] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-mannosidase Beta-mannosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.25 3.2.1.25] </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=2vmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vmf OCA], [http://pdbe.org/2vmf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vmf RCSB], [http://www.ebi.ac.uk/pdbsum/2vmf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vmf 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=2vmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vmf OCA], [http://pdbe.org/2vmf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vmf RCSB], [http://www.ebi.ac.uk/pdbsum/2vmf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vmf ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	==See Also==		==See Also==
	*[[Mannosidase\|Mannosidase]]		*[[Mannosidase 3D structures\|Mannosidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Bactn]]		[[Category: Bactn]]
	[[Category: Beta-mannosidase]]		[[Category: Beta-mannosidase]]
			[[Category: Large Structures]]
	[[Category: Bleriot, Y]]		[[Category: Bleriot, Y]]
	[[Category: Davies, G J]]		[[Category: Davies, G J]]

OCA at 20:32, 19 September 2018

2018-09-19T20:32:58Z

← Older revision		Revision as of 20:32, 19 September 2018
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	==~~STRUCTURAL AND BIOCHEMICAL EVIDENCE FOR A BOAT~~-~~LIKE TRANSITION STATE IN BETA~~-~~MANNOSIDASES~~==		==Structural and biochemical evidence for a boat-like transition state in beta-mannosidases==
	<StructureSection load='2vmf' size='340' side='right' caption='[[2vmf]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2vmf' size='340' side='right' caption='[[2vmf]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
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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/vm/2vmf_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vm/2vmf_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>

OCA at 19:35, 11 August 2016

2016-08-11T19:35:39Z

← Older revision		Revision as of 19:35, 11 August 2016
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	==STRUCTURAL AND BIOCHEMICAL EVIDENCE FOR A BOAT-LIKE TRANSITION STATE IN BETA-MANNOSIDASES==		==STRUCTURAL AND BIOCHEMICAL EVIDENCE FOR A BOAT-LIKE TRANSITION STATE IN BETA-MANNOSIDASES==
	<StructureSection load='2vmf' size='340' side='right' caption='[[2vmf]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2vmf' size='340' side='right' caption='[[2vmf]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2vmf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VMF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VMF FirstGlance]. <br>		<table><tr><td colspan='2'>[[2vmf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bactn Bactn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VMF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VMF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MVL:(5R,6R,7S,8R)-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL'>MVL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MVL:(5R,6R,7S,8R)-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL'>MVL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2vqt\|2vqt]], [[2vot\|2vot]], [[2vl4\|2vl4]], [[2vqu\|2vqu]], [[2vo5\|2vo5]], [[2je8\|2je8]], [[2vjx\|2vjx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2vqt\|2vqt]], [[2vot\|2vot]], [[2vl4\|2vl4]], [[2vqu\|2vqu]], [[2vo5\|2vo5]], [[2je8\|2je8]], [[2vjx\|2vjx]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-mannosidase Beta-mannosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.25 3.2.1.25] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-mannosidase Beta-mannosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.25 3.2.1.25] </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=2vmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vmf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vmf RCSB], [http://www.ebi.ac.uk/pdbsum/2vmf 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=2vmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vmf OCA], [http://pdbe.org/2vmf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vmf RCSB], [http://www.ebi.ac.uk/pdbsum/2vmf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vmf ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	<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=2vmf 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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	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 2vmf" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Bacteroides thetaiotaomicron~~]]		[[Category: Bactn]]
	[[Category: Beta-mannosidase]]		[[Category: Beta-mannosidase]]
	[[Category: Bleriot, Y]]		[[Category: Bleriot, Y]]

OCA at 16:12, 19 January 2015

2015-01-19T16:12:30Z

← Older revision		Revision as of 16:12, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2vmf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VMF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VMF FirstGlance]. <br>		<table><tr><td colspan='2'>[[2vmf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VMF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VMF FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MVL:(5R,6R,7S,8R)-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL'>MVL</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MVL:(5R,6R,7S,8R)-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL'>MVL</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2vqt\|2vqt]], [[2vot\|2vot]], [[2vl4\|2vl4]], [[2vqu\|2vqu]], [[2vo5\|2vo5]], [[2je8\|2je8]], [[2vjx\|2vjx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2vqt\|2vqt]], [[2vot\|2vot]], [[2vl4\|2vl4]], [[2vqu\|2vqu]], [[2vo5\|2vo5]], [[2je8\|2je8]], [[2vjx\|2vjx]]</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-mannosidase Beta-mannosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.25 3.2.1.25] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-mannosidase Beta-mannosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.25 3.2.1.25] </span></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=2vmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vmf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vmf RCSB], [http://www.ebi.ac.uk/pdbsum/2vmf 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=2vmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vmf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vmf RCSB], [http://www.ebi.ac.uk/pdbsum/2vmf 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 35:		Line 35:
	[[Category: Bacteroides thetaiotaomicron]]		[[Category: Bacteroides thetaiotaomicron]]
	[[Category: Beta-mannosidase]]		[[Category: Beta-mannosidase]]
	[[Category: Bleriot, Y.]]		[[Category: Bleriot, Y]]
	[[Category: Davies, G J.]]		[[Category: Davies, G J]]
	[[Category: Dumon, C.]]		[[Category: Dumon, C]]
	[[Category: Gilbert, H J.]]		[[Category: Gilbert, H J]]
	[[Category: Gratien, J.]]		[[Category: Gratien, J]]
	[[Category: Heck, M P.]]		[[Category: Heck, M P]]
	[[Category: Moreland, C.]]		[[Category: Moreland, C]]
	[[Category: Offen, W A.]]		[[Category: Offen, W A]]
	[[Category: Smith, N L.]]		[[Category: Smith, N L]]
	[[Category: Stick, R V.]]		[[Category: Stick, R V]]
	[[Category: Tailford, L E.]]		[[Category: Tailford, L E]]
	[[Category: Vasella, A.]]		[[Category: Vasella, A]]
	[[Category: Glycoside hydrolase]]		[[Category: Glycoside hydrolase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 08:21, 29 September 2014

2014-09-29T08:21:56Z

← Older revision		Revision as of 08:21, 29 September 2014
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	[[Image:~~2vmf~~.~~png~~\|~~left~~\|~~200px~~]]		==STRUCTURAL AND BIOCHEMICAL EVIDENCE FOR A BOAT-LIKE TRANSITION STATE IN BETA-MANNOSIDASES==
			<StructureSection load='2vmf' size='340' side='right' caption='[[2vmf]], [[Resolution\|resolution]] 2.10Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2vmf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VMF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VMF FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MVL:(5R,6R,7S,8R)-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL'>MVL</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2vqt\|2vqt]], [[2vot\|2vot]], [[2vl4\|2vl4]], [[2vqu\|2vqu]], [[2vo5\|2vo5]], [[2je8\|2je8]], [[2vjx\|2vjx]]</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-mannosidase Beta-mannosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.25 3.2.1.25] </span></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=2vmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vmf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vmf RCSB], [http://www.ebi.ac.uk/pdbsum/2vmf 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/vm/2vmf_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 ==
			Enzyme inhibition through mimicry of the transition state is a major area for the design of new therapeutic agents. Emerging evidence suggests that many retaining glycosidases that are active on alpha- or beta-mannosides harness unusual B2,5 (boat) transition states. Here we present the analysis of 25 putative beta-mannosidase inhibitors, whose Ki values range from nanomolar to millimolar, on the Bacteroides thetaiotaomicron beta-mannosidase BtMan2A. B2,5 or closely related conformations were observed for all tightly binding compounds. Subsequent linear free energy relationships that correlate log Ki with log Km/kcat for a series of active center variants highlight aryl-substituted mannoimidazoles as powerful transition state mimics in which the binding energy of the aryl group enhances both binding and the degree of transition state mimicry. Support for a B2,5 transition state during enzymatic beta-mannosidase hydrolysis should also facilitate the design and exploitation of transition state mimics for the inhibition of retaining alpha-mannosidases--an area that is emerging for anticancer therapeutics.

	~~{{STRUCTURE_2vmf\| PDB=2vmf \| SCENE= }}~~		Structural and biochemical evidence for a boat-like transition state in beta-mannosidases.,Tailford LE, Offen WA, Smith NL, Dumon C, Morland C, Gratien J, Heck MP, Stick RV, Bleriot Y, Vasella A, Gilbert HJ, Davies GJ Nat Chem Biol. 2008 May;4(5):306-12. PMID:18408714<ref>PMID:18408714</ref>

	~~===STRUCTURAL AND BIOCHEMICAL EVIDENCE FOR A BOAT-LIKE TRANSITION STATE IN BETA-MANNOSIDASES===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_18408714}}~~

	~~==About this Structure==~~
	~~[[2vmf]] is~~ a ~~2 chain structure with sequence from [http://en.wikipedia~~.~~org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann.ac.il/oca-bin~~/~~ocashort?id=2VMF OCA].~~

	==See Also==		==See Also==
	*[[Mannosidase\|Mannosidase]]		*[[Mannosidase\|Mannosidase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:018408714<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Bacteroides thetaiotaomicron]]		[[Category: Bacteroides thetaiotaomicron]]
	[[Category: Beta-mannosidase]]		[[Category: Beta-mannosidase]]

OCA at 17:39, 20 October 2012

2012-10-20T17:39:57Z

← Older revision		Revision as of 17:39, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[2vmf]] is a 2 chain structure ~~of [[Mannosidase]]~~ with sequence from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VMF OCA].		[[2vmf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VMF OCA].

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

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

2012-07-27T01:38:08Z

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

← Older revision	Revision as of 01:38, 27 July 2012
(No difference)

OCA at 01:38, 27 July 2012

2012-07-27T01:38:07Z

← Older revision		Revision as of 01:38, 27 July 2012
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	~~{{Seed}}~~
	[[Image:2vmf.png\|left\|200px]]		[[Image:2vmf.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2vmf", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_2vmf\| PDB=2vmf \| SCENE= }}		{{STRUCTURE_2vmf\| PDB=2vmf \| SCENE= }}

	===STRUCTURAL AND BIOCHEMICAL EVIDENCE FOR A BOAT-LIKE TRANSITION STATE IN BETA-MANNOSIDASES===		===STRUCTURAL AND BIOCHEMICAL EVIDENCE FOR A BOAT-LIKE TRANSITION STATE IN BETA-MANNOSIDASES===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_18408714}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 18408714 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_18408714}}		{{ABSTRACT_PUBMED_18408714}}

	==About this Structure==		==About this Structure==
	~~2VMF~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VMF OCA].		[[2vmf]] is a 2 chain structure of [[Mannosidase]] with sequence from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VMF OCA].

			==See Also==
			*[[Mannosidase\|Mannosidase]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~18408714~~</ref><references group="xtra"/>		<ref group="xtra">PMID:018408714</ref><references group="xtra"/>
	[[Category: Bacteroides thetaiotaomicron]]		[[Category: Bacteroides thetaiotaomicron]]
	[[Category: Beta-mannosidase]]		[[Category: Beta-mannosidase]]
Line 43:		Line 34:
	[[Category: Mannosidase]]		[[Category: Mannosidase]]
	[[Category: Transition state mimic]]		[[Category: Transition state mimic]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:20:53 2009''~~

OCA at 16:20, 17 February 2009

2009-02-17T16:20:56Z

← Older revision		Revision as of 16:20, 17 February 2009
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	==About this Structure==		==About this Structure==
	2VMF is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VMF OCA].		2VMF is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VMF OCA].

	==Reference==		==Reference==
	Structural and biochemical evidence for a boat-like transition state in beta-mannosidases., Tailford LE, Offen WA, Smith NL, Dumon C, Morland C, Gratien J, Heck MP, Stick RV, Bleriot Y, Vasella A, Gilbert HJ, Davies GJ, Nat Chem Biol. 2008 May;4(5):306-12. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18408714 18408714]~~		<ref group="xtra">PMID:18408714</ref><references group="xtra"/>
	[[Category: Bacteroides thetaiotaomicron]]		[[Category: Bacteroides thetaiotaomicron]]
	[[Category: Beta-mannosidase]]		[[Category: Beta-mannosidase]]
	~~[[Category: Single protein]]~~
	[[Category: Bleriot, Y.]]		[[Category: Bleriot, Y.]]
	[[Category: Davies, G J.]]		[[Category: Davies, G J.]]
Line 45:		Line 44:
	[[Category: Transition state mimic]]		[[Category: Transition state mimic]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 02~~:16:~~43 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:20:53 2009''