2vot - Revision history

OCA at 15:27, 13 December 2023

OCA — Wed, 13 Dec 2023 15:27:07 GMT

←Older revision		Revision as of 15:27, 13 December 2023
Line 3:		Line 3:
	<StructureSection load='2vot' size='340' side='right'caption='[[2vot]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='2vot' size='340' side='right'caption='[[2vot]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2vot]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bactn Bactn~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VOT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VOT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2vot]] 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=2VOT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VOT 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=NHV:(5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(HYDROXYMETHYL)-2-[(PHENYLAMINO)METHYL]-5,6,7,8-TETRAHYDRO-1H-IMIDAZO[1,2-A]PYRIDIN-4-IUM'>NHV</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]] 1.95Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2vqt\|2vqt]], [[2vl4\|2vl4]], [[2vqu\|2vqu]], [[2vo5\|2vo5]], [[2je8\|2je8]], [[2vjx\|2vjx]], [[2vmf\|2vmf]]</div></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=NHV:(5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(HYDROXYMETHYL)-2-[(PHENYLAMINO)METHYL]-5,6,7,8-TETRAHYDRO-1H-IMIDAZO[1,2-A]PYRIDIN-4-IUM'>NHV</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-mannosidase Beta-mannosidase], with EC number [https://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=2vot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vot OCA], [https://pdbe.org/2vot PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vot RCSB], [https://www.ebi.ac.uk/pdbsum/2vot PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vot 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=2vot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vot OCA], [https://pdbe.org/2vot PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vot RCSB], [https://www.ebi.ac.uk/pdbsum/2vot PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vot 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]]
Line 35:		Line 36:
	__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 M-P]]
-	[[Category: Moreland, C]]	+	[[Category: Moreland C]]
-	[[Category: Offen~~, W A~~]]	+	[[Category: Offen WA]]
-	[[Category: Smith, N]]	+	[[Category: Smith N]]
-	[[Category: Stick~~, R V~~]]	+	[[Category: Stick RV]]
-	[[Category: Tailford~~, L N~~]]	+	[[Category: Tailford LN]]
-	[[Category: Vasella, A]]	+	[[Category: Vasella A]]
-	~~[[Category: Glycoside hydrolase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Linear free energy relationship]]~~	+
-	~~[[Category: Mannosidase]]~~	+
-	~~[[Category: Transition state mimic~~]]	+

OCA at 11:42, 30 March 2022

OCA — Wed, 30 Mar 2022 11:42:31 GMT

←Older revision		Revision as of 11:42, 30 March 2022
Line 3:		Line 3:
	<StructureSection load='2vot' size='340' side='right'caption='[[2vot]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='2vot' size='340' side='right'caption='[[2vot]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2vot]] 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=2VOT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2VOT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2vot]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bactn Bactn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VOT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VOT 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=NHV:(5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(HYDROXYMETHYL)-2-[(PHENYLAMINO)METHYL]-5,6,7,8-TETRAHYDRO-1H-IMIDAZO[1,2-A]PYRIDIN-4-IUM'>NHV</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=NHV:(5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(HYDROXYMETHYL)-2-[(PHENYLAMINO)METHYL]-5,6,7,8-TETRAHYDRO-1H-IMIDAZO[1,2-A]PYRIDIN-4-IUM'>NHV</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2vqt\|2vqt]], [[2vl4\|2vl4]], [[2vqu\|2vqu]], [[2vo5\|2vo5]], [[2je8\|2je8]], [[2vjx\|2vjx]], [[2vmf\|2vmf]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2vqt\|2vqt]], [[2vl4\|2vl4]], [[2vqu\|2vqu]], [[2vo5\|2vo5]], [[2je8\|2je8]], [[2vjx\|2vjx]], [[2vmf\|2vmf]]</div></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'>[https://en.wikipedia.org/wiki/Beta-mannosidase Beta-mannosidase], with EC number [https://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~~://proteopedia.org/fgij/fg.htm?mol=2vot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vot OCA], [~~http~~://pdbe.org/2vot PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2vot RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2vot PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2vot 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=2vot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vot OCA], [https://pdbe.org/2vot PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vot RCSB], [https://www.ebi.ac.uk/pdbsum/2vot PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vot ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 08:16, 25 June 2020

OCA — Thu, 25 Jun 2020 08:16:37 GMT

←Older revision		Revision as of 08:16, 25 June 2020
Line 1:		Line 1:

	==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='2vot' size='340' side='right' caption='[[2vot]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='2vot' size='340' side='right'caption='[[2vot]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2vot]] 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=2VOT OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2VOT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2vot]] 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=2VOT OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2VOT 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=NHV:(5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(HYDROXYMETHYL)-2-[(PHENYLAMINO)METHYL]-5,6,7,8-TETRAHYDRO-1H-IMIDAZO[1,2-A]PYRIDIN-4-IUM'>NHV</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=NHV:(5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(HYDROXYMETHYL)-2-[(PHENYLAMINO)METHYL]-5,6,7,8-TETRAHYDRO-1H-IMIDAZO[1,2-A]PYRIDIN-4-IUM'>NHV</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2vqt\|2vqt]], [[2vl4\|2vl4]], [[2vqu\|2vqu]], [[2vo5\|2vo5]], [[2je8\|2je8]], [[2vjx\|2vjx]], [[2vmf\|2vmf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2vqt\|2vqt]], [[2vl4\|2vl4]], [[2vqu\|2vqu]], [[2vo5\|2vo5]], [[2je8\|2je8]], [[2vjx\|2vjx]], [[2vmf\|2vmf]]</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=2vot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vot OCA], [http://pdbe.org/2vot PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vot RCSB], [http://www.ebi.ac.uk/pdbsum/2vot PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vot 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=2vot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vot OCA], [http://pdbe.org/2vot PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vot RCSB], [http://www.ebi.ac.uk/pdbsum/2vot PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vot ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Mannosidase\|Mannosidase]]	+	*[[Mannosidase 3D structures\|Mannosidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 37:
	[[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 21:07, 19 September 2018

OCA — Wed, 19 Sep 2018 21:07:34 GMT

←Older revision		Revision as of 21:07, 19 September 2018
Line 1:		Line 1:
-	==~~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='2vot' size='340' side='right' caption='[[2vot]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='2vot' size='340' side='right' caption='[[2vot]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2vqt\|2vqt]], [[2vl4\|2vl4]], [[2vqu\|2vqu]], [[2vo5\|2vo5]], [[2je8\|2je8]], [[2vjx\|2vjx]], [[2vmf\|2vmf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2vqt\|2vqt]], [[2vl4\|2vl4]], [[2vqu\|2vqu]], [[2vo5\|2vo5]], [[2je8\|2je8]], [[2vjx\|2vjx]], [[2vmf\|2vmf]]</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=2vot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vot OCA], [http://pdbe.org/2vot PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vot RCSB], [http://www.ebi.ac.uk/pdbsum/2vot 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=2vot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vot OCA], [http://pdbe.org/2vot PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vot RCSB], [http://www.ebi.ac.uk/pdbsum/2vot PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vot ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vo/2vot_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vo/2vot_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 01:09, 8 February 2016

OCA — Mon, 08 Feb 2016 01:09:45 GMT

←Older revision		Revision as of 01:09, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='2vot' size='340' side='right' caption='[[2vot]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='2vot' size='340' side='right' caption='[[2vot]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2vot]] 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=2VOT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VOT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2vot]] 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=2VOT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VOT 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=NHV:(5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(HYDROXYMETHYL)-2-[(PHENYLAMINO)METHYL]-5,6,7,8-TETRAHYDRO-1H-IMIDAZO[1,2-A]PYRIDIN-4-IUM'>NHV</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=NHV:(5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(HYDROXYMETHYL)-2-[(PHENYLAMINO)METHYL]-5,6,7,8-TETRAHYDRO-1H-IMIDAZO[1,2-A]PYRIDIN-4-IUM'>NHV</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2vqt\|2vqt]], [[2vl4\|2vl4]], [[2vqu\|2vqu]], [[2vo5\|2vo5]], [[2je8\|2je8]], [[2vjx\|2vjx]], [[2vmf\|2vmf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2vqt\|2vqt]], [[2vl4\|2vl4]], [[2vqu\|2vqu]], [[2vo5\|2vo5]], [[2je8\|2je8]], [[2vjx\|2vjx]], [[2vmf\|2vmf]]</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=2vot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vot OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vot RCSB], [http://www.ebi.ac.uk/pdbsum/2vot 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=2vot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vot OCA], [http://pdbe.org/2vot PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vot RCSB], [http://www.ebi.ac.uk/pdbsum/2vot PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 16:
	<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=2vot ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 26:
	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 2vot" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacteroides thetaiotaomicron~~]]	+	[[Category: Bactn]]
	[[Category: Beta-mannosidase]]		[[Category: Beta-mannosidase]]
	[[Category: Bleriot, Y]]		[[Category: Bleriot, Y]]

OCA at 18:15, 19 January 2015

OCA — Mon, 19 Jan 2015 18:15:53 GMT

←Older revision		Revision as of 18:15, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2vot]] 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=2VOT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VOT FirstGlance]. <br>		<table><tr><td colspan='2'>[[2vot]] 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=2VOT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VOT 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=NHV:(5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(HYDROXYMETHYL)-2-[(PHENYLAMINO)METHYL]-5,6,7,8-TETRAHYDRO-1H-IMIDAZO[1,2-A]PYRIDIN-4-IUM'>NHV</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=NHV:(5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(HYDROXYMETHYL)-2-[(PHENYLAMINO)METHYL]-5,6,7,8-TETRAHYDRO-1H-IMIDAZO[1,2-A]PYRIDIN-4-IUM'>NHV</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2vqt\|2vqt]], [[2vl4\|2vl4]], [[2vqu\|2vqu]], [[2vo5\|2vo5]], [[2je8\|2je8]], [[2vjx\|2vjx]], [[2vmf\|2vmf]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2vqt\|2vqt]], [[2vl4\|2vl4]], [[2vqu\|2vqu]], [[2vo5\|2vo5]], [[2je8\|2je8]], [[2vjx\|2vjx]], [[2vmf\|2vmf]]</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=2vot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vot OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vot RCSB], [http://www.ebi.ac.uk/pdbsum/2vot 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=2vot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vot OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vot RCSB], [http://www.ebi.ac.uk/pdbsum/2vot 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.]]	+	[[Category: Smith, N]]
-	[[Category: Stick, R V.]]	+	[[Category: Stick, R V]]
-	[[Category: Tailford, L N.]]	+	[[Category: Tailford, L N]]
-	[[Category: Vasella, A.]]	+	[[Category: Vasella, A]]
	[[Category: Glycoside hydrolase]]		[[Category: Glycoside hydrolase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 10:10, 29 September 2014

OCA — Mon, 29 Sep 2014 10:10:02 GMT

←Older revision		Revision as of 10:10, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2vot.~~png~~\|~~left~~\|200px]]	+	==STRUCTURAL AND BIOCHEMICAL EVIDENCE FOR A BOAT-LIKE TRANSITION STATE IN BETA-MANNOSIDASES==
		+	<StructureSection load='2vot' size='340' side='right' caption='[[2vot]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2vot]] 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=2VOT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VOT 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=NHV:(5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(HYDROXYMETHYL)-2-[(PHENYLAMINO)METHYL]-5,6,7,8-TETRAHYDRO-1H-IMIDAZO[1,2-A]PYRIDIN-4-IUM'>NHV</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2vqt\|2vqt]], [[2vl4\|2vl4]], [[2vqu\|2vqu]], [[2vo5\|2vo5]], [[2je8\|2je8]], [[2vjx\|2vjx]], [[2vmf\|2vmf]]</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=2vot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vot OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vot RCSB], [http://www.ebi.ac.uk/pdbsum/2vot 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/vo/2vot_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_2vot\| PDB=2vot \| 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==~~	+
-	~~[[2vot]] 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=2VOT 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 08:24, 20 October 2012

OCA — Sat, 20 Oct 2012 08:24:18 GMT

←Older revision		Revision as of 08:24, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2vot]] 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=2VOT OCA].	+	[[2vot]] 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=2VOT OCA].

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

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

OCA — Wed, 25 Jul 2012 19:25:04 GMT

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

←Older revision

Revision as of 19:25, 25 July 2012

OCA at 19:25, 25 July 2012

OCA — Wed, 25 Jul 2012 19:25:03 GMT

←Older revision		Revision as of 19:25, 25 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2vot.png\|left\|200px]]		[[Image:2vot.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2vot", 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_2vot\| PDB=2vot \| SCENE= }}		{{STRUCTURE_2vot\| PDB=2vot \| 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===

		+	{{ABSTRACT_PUBMED_18408714}}

	==About this Structure==		==About this Structure==
-	~~2VOT~~ 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=2VOT OCA].	+	[[2vot]] 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=2VOT OCA].
		+
		+	==See Also==
		+	*[[Mannosidase\|Mannosidase]]
		+
		+	==Reference==
		+	<ref group="xtra">PMID:018408714</ref><references group="xtra"/>
	[[Category: Bacteroides thetaiotaomicron]]		[[Category: Bacteroides thetaiotaomicron]]
	[[Category: Beta-mannosidase]]		[[Category: Beta-mannosidase]]
Line 34:		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 Mon Feb 16 17:43:06 2009''