5n6s - Revision history

OCA at 12:29, 15 November 2023

OCA — Wed, 15 Nov 2023 12:29:57 GMT

←Older revision		Revision as of 12:29, 15 November 2023
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	<StructureSection load='5n6s' size='340' side='right'caption='[[5n6s]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5n6s' size='340' side='right'caption='[[5n6s]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5n6s]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_43589 Atcc 43589~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N6S OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5N6S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5n6s]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N6S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5N6S FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8P5:AZANYLIDENE-[4-[[(1~{S},2~{R},3~{R},4~{R},5~{S},6~{S},7~{S})-2-(HYDROXYMETHYL)-3,4,5-TRIS(OXIDANYL)-7-BICYCLO[4.1.0]HEPTANYL]CARBONYLAMINO]BUTYLIMINO]AZANIUM'>8P5</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bglA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8P5:AZANYLIDENE-[4-[[(1~{S},2~{R},3~{R},4~{R},5~{S},6~{S},7~{S})-2-(HYDROXYMETHYL)-3,4,5-TRIS(OXIDANYL)-7-BICYCLO[4.1.0]HEPTANYL]CARBONYLAMINO]BUTYLIMINO]AZANIUM'>8P5</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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-glucosidase Beta-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.21 3.2.1.21] </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=5n6s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n6s OCA], [https://pdbe.org/5n6s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5n6s RCSB], [https://www.ebi.ac.uk/pdbsum/5n6s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5n6s 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=5n6s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n6s OCA], [~~http~~://pdbe.org/5n6s PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5n6s RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5n6s PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5n6s ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/BGLA_THEMA BGLA_THEMA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 43589]]
-	[[Category: Beta-glucosidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Davies, G~~]]	+	[[Category: Thermotoga maritima]]
-	[[Category: ~~Offen, W~~]]	+	[[Category: Davies G]]
-	[[Category: ~~Carba-cyclophellitol]]~~	+	[[Category: Offen W]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Mimic~~]]	+

OCA at 11:58, 26 August 2020

OCA — Wed, 26 Aug 2020 11:58:01 GMT

←Older revision		Revision as of 11:58, 26 August 2020
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	==Thermotoga maritima family 1 Glycoside hydrolase complexed with Carba-Cyclophellitol transition state mimic==		==Thermotoga maritima family 1 Glycoside hydrolase complexed with Carba-Cyclophellitol transition state mimic==
-	<StructureSection load='5n6s' size='340' side='right' caption='[[5n6s]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5n6s' size='340' side='right'caption='[[5n6s]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5n6s]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N6S OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5N6S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5n6s]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N6S OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5N6S FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8P5:AZANYLIDENE-[4-[[(1~{S},2~{R},3~{R},4~{R},5~{S},6~{S},7~{S})-2-(HYDROXYMETHYL)-3,4,5-TRIS(OXIDANYL)-7-BICYCLO[4.1.0]HEPTANYL]CARBONYLAMINO]BUTYLIMINO]AZANIUM'>8P5</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8P5:AZANYLIDENE-[4-[[(1~{S},2~{R},3~{R},4~{R},5~{S},6~{S},7~{S})-2-(HYDROXYMETHYL)-3,4,5-TRIS(OXIDANYL)-7-BICYCLO[4.1.0]HEPTANYL]CARBONYLAMINO]BUTYLIMINO]AZANIUM'>8P5</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bglA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-glucosidase Beta-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.21 3.2.1.21] </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-glucosidase Beta-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.21 3.2.1.21] </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=5n6s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n6s OCA], [http://pdbe.org/5n6s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n6s RCSB], [http://www.ebi.ac.uk/pdbsum/5n6s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n6s 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=5n6s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n6s OCA], [http://pdbe.org/5n6s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n6s RCSB], [http://www.ebi.ac.uk/pdbsum/5n6s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n6s ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 20:

	==See Also==		==See Also==
-	*[[Beta-glucosidase\|Beta-glucosidase]]	+	*[[Beta-glucosidase 3D structures\|Beta-glucosidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 43589]]
	[[Category: Beta-glucosidase]]		[[Category: Beta-glucosidase]]
		+	[[Category: Large Structures]]
	[[Category: Davies, G]]		[[Category: Davies, G]]
	[[Category: Offen, W]]		[[Category: Offen, W]]

OCA at 09:09, 17 May 2017

OCA — Wed, 17 May 2017 09:09:59 GMT

←Older revision		Revision as of 09:09, 17 May 2017
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	<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=5n6s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n6s OCA], [http://pdbe.org/5n6s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n6s RCSB], [http://www.ebi.ac.uk/pdbsum/5n6s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n6s 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=5n6s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n6s OCA], [http://pdbe.org/5n6s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n6s RCSB], [http://www.ebi.ac.uk/pdbsum/5n6s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n6s ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The conformational analysis of glycosidases affords a route to their specific inhibition through transition-state mimicry. Inspired by the rapid reaction rates of cyclophellitol and cyclophellitol aziridine-both covalent retaining beta-glucosidase inhibitors-we postulated that the corresponding carba "cyclopropyl" analogue would be a potent retaining beta-glucosidase inhibitor for those enzymes reacting through the 4H3 transition-state conformation. Ab initio metadynamics simulations of the conformational free energy landscape for the cyclopropyl inhibitors show a strong bias for the 4H3 conformation, and carba-cyclophellitol, with an N-(4-azidobutyl)carboxamide moiety, proved to be a potent inhibitor (Ki = 8.2 nM) of the Thermotoga maritima TmGH1 beta-glucosidase. 3-D structural analysis and comparison with unreacted epoxides show that this compound indeed binds in the 4H3 conformation, suggesting that conformational strain induced through a cyclopropyl unit may add to the armory of tight-binding inhibitor designs.
		+
		+	Carba-cyclophellitols Are Neutral Retaining-Glucosidase Inhibitors.,Beenakker TJM, Wander DPA, Offen WA, Artola M, Raich L, Ferraz MJ, Li KY, Houben JHPM, van Rijssel ER, Hansen T, van der Marel GA, Codee JDC, Aerts JMFG, Rovira C, Davies GJ, Overkleeft HS J Am Chem Soc. 2017 May 5. doi: 10.1021/jacs.7b01773. PMID:28463498<ref>PMID:28463498</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5n6s" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Beta-glucosidase\|Beta-glucosidase]]		*[[Beta-glucosidase\|Beta-glucosidase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:24, 10 May 2017

OCA — Wed, 10 May 2017 06:24:43 GMT

←Older revision		Revision as of 06:24, 10 May 2017
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	<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=5n6s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n6s OCA], [http://pdbe.org/5n6s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n6s RCSB], [http://www.ebi.ac.uk/pdbsum/5n6s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n6s 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=5n6s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n6s OCA], [http://pdbe.org/5n6s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n6s RCSB], [http://www.ebi.ac.uk/pdbsum/5n6s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n6s ProSAT]</span></td></tr>
	</table>		</table>
		+
		+	==See Also==
		+	*[[Beta-glucosidase\|Beta-glucosidase]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA: Protected "5n6s" [edit=sysop:move=sysop]

OCA — Sat, 11 Mar 2017 09:39:16 GMT

Protected "5n6s" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:39, 11 March 2017

OCA: New page: ==Thermotoga maritima family 1 Glycoside hydrolase complexed with Carba-Cyclophellitol transition state mimic== == Structural highlights ==
<table><tr><td colspan='2'>[[5n6s]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N6S OCA]. For a guided tour on the structure components use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5N6S FirstGlance]. 
</td></tr><tr id='ligand'><td class="sblockLbl">[[Ligand|Ligands:]]</td><td class="sblockDat"><scene name='pdbligand=8P5:AZANYLIDENE-[4-[[(1~{S},2~{R},3~{R},4~{R},5~{S},6~{S},7~{S})-2-(HYDROXYMETHYL)-3,4,5-TRIS(OXIDANYL)-7-BICYCLO[4.1.0]HEPTANYL]CARBONYLAMINO]BUTYLIMINO]AZANIUM'>8P5</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
<tr id='activity'><td class="sblockLbl">Activity:</td><td class="sblockDat">[http://en.wikipedia.org/wiki/Beta-glucosidase Beta-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.21 3.2.1.21] </td></tr>
<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5n6s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n6s OCA], [http://pdbe.org/5n6s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n6s RCSB], [http://www.ebi.ac.uk/pdbsum/5n6s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n6s ProSAT]</td></tr>
</table>
TOC
</StructureSection>
[[Category: Beta-glucosidase]]
[[Category: Davies, G]]
[[Category: Offen, W]]
[[Category: Carba-cyclophellitol]]
[[Category: Hydrolase]]
[[Category: Mimic]]