5m12 - Revision history

OCA at 18:19, 1 November 2023

OCA — Wed, 01 Nov 2023 18:19:40 GMT

←Older revision		Revision as of 18:19, 1 November 2023
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	<StructureSection load='5m12' size='340' side='right'caption='[[5m12]], [[Resolution\|resolution]] 1.53Å' scene=''>		<StructureSection load='5m12' size='340' side='right'caption='[[5m12]], [[Resolution\|resolution]] 1.53Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5m12]] is a 1 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=5M12 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5M12 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5m12]] is a 1 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=5M12 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5M12 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7D0:(1~{R},2~{S},3~{S},4~{R},5~{S},6~{S})-5-[3,5-BIS(FLUORANYL)PHENOXY]-1-(HYDROXYMETHYL)BICYCLO[4.1.0]HEPTANE-2,3,4-TRIOL'>7D0</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.53Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">galA ([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=7D0:(1~{R},2~{S},3~{S},4~{R},5~{S},6~{S})-5-[3,5-BIS(FLUORANYL)PHENOXY]-1-(HYDROXYMETHYL)BICYCLO[4.1.0]HEPTANE-2,3,4-TRIOL'>7D0</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-galactosidase Alpha-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.22 3.2.1.22] </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=5m12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m12 OCA], [https://pdbe.org/5m12 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5m12 RCSB], [https://www.ebi.ac.uk/pdbsum/5m12 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5m12 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=5m12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m12 OCA], [~~http~~://pdbe.org/5m12 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5m12 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5m12 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5m12 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/AGAL_THEMA AGAL_THEMA] Hydrolyzes the short-chain alpha-galactosaccharides raffinose, melibiose and stachyose.<ref>PMID:25486100</ref> <ref>PMID:9741105</ref>
	<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: Alpha-galactosidase]]
-	[[Category: Atcc 43589]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Gloster, T~~]]	+	[[Category: Thermotoga maritima]]
-	[[Category: ~~Pengelly, R~~]]	+	[[Category: Gloster T]]
-	[[Category: ~~Glycoside hydrolase]]~~	+	[[Category: Pengelly R]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 10:57, 12 August 2020

OCA — Wed, 12 Aug 2020 10:57:52 GMT

←Older revision		Revision as of 10:57, 12 August 2020
Line 1:		Line 1:

	==Structure of GH36 alpha-galactosidase from Thermotoga maritima in complex with intact cyclopropyl-carbasugar.==		==Structure of GH36 alpha-galactosidase from Thermotoga maritima in complex with intact cyclopropyl-carbasugar.==
-	<StructureSection load='5m12' size='340' side='right' caption='[[5m12]], [[Resolution\|resolution]] 1.53Å' scene=''>	+	<StructureSection load='5m12' size='340' side='right'caption='[[5m12]], [[Resolution\|resolution]] 1.53Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5m12]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M12 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5M12 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5m12]] is a 1 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=5M12 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5M12 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7D0:(1~{R},2~{S},3~{S},4~{R},5~{S},6~{S})-5-[3,5-BIS(FLUORANYL)PHENOXY]-1-(HYDROXYMETHYL)BICYCLO[4.1.0]HEPTANE-2,3,4-TRIOL'>7D0</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7D0:(1~{R},2~{S},3~{S},4~{R},5~{S},6~{S})-5-[3,5-BIS(FLUORANYL)PHENOXY]-1-(HYDROXYMETHYL)BICYCLO[4.1.0]HEPTANE-2,3,4-TRIOL'>7D0</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">galA ([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/Alpha-galactosidase Alpha-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.22 3.2.1.22] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-galactosidase Alpha-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.22 3.2.1.22] </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=5m12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m12 OCA], [http://pdbe.org/5m12 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m12 RCSB], [http://www.ebi.ac.uk/pdbsum/5m12 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m12 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=5m12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m12 OCA], [http://pdbe.org/5m12 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m12 RCSB], [http://www.ebi.ac.uk/pdbsum/5m12 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m12 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5m12" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5m12" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Galactosidase 3D structures\|Galactosidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Alpha-galactosidase]]		[[Category: Alpha-galactosidase]]
		+	[[Category: Atcc 43589]]
		+	[[Category: Large Structures]]
	[[Category: Gloster, T]]		[[Category: Gloster, T]]
	[[Category: Pengelly, R]]		[[Category: Pengelly, R]]
	[[Category: Glycoside hydrolase]]		[[Category: Glycoside hydrolase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 19:57, 9 December 2016

OCA — Fri, 09 Dec 2016 19:57:43 GMT

←Older revision		Revision as of 19:57, 9 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5m12 is ~~ON HOLD~~	+	==Structure of GH36 alpha-galactosidase from Thermotoga maritima in complex with intact cyclopropyl-carbasugar.==
		+	<StructureSection load='5m12' size='340' side='right' caption='[[5m12]], [[Resolution\|resolution]] 1.53Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5m12]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M12 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5M12 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7D0:(1~{R},2~{S},3~{S},4~{R},5~{S},6~{S})-5-[3,5-BIS(FLUORANYL)PHENOXY]-1-(HYDROXYMETHYL)BICYCLO[4.1.0]HEPTANE-2,3,4-TRIOL'>7D0</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-galactosidase Alpha-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.22 3.2.1.22] </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=5m12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m12 OCA], [http://pdbe.org/5m12 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m12 RCSB], [http://www.ebi.ac.uk/pdbsum/5m12 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m12 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Glycoside hydrolases (GHs) have attracted considerable attention as targets for therapeutic agents, and thus mechanism-based inhibitors are of great interest. We report the first structural analysis of a carbocyclic mechanism-based GH inactivator, the results of which show that the two Michaelis complexes are in 2 H3 conformations. We also report the synthesis and reactivity of a fluorinated analogue and the structure of its covalently linked intermediate (flattened 2 H3 half-chair). We conclude that these inactivator reactions mainly involve motion of the pseudo-anomeric carbon atom, knowledge that should stimulate the design of new transition-state analogues for use as chemical biology tools.

-	~~Authors:~~ Pengelly, R., Gloster, T.	+	Structural Snapshots for Mechanism-Based Inactivation of a Glycoside Hydrolase by Cyclopropyl Carbasugars.,Adamson C, Pengelly RJ, Shamsi Kazem Abadi S, Chakladar S, Draper J, Britton R, Gloster TM, Bennet AJ Angew Chem Int Ed Engl. 2016 Nov 21;55(48):14978-14982. doi:, 10.1002/anie.201607431. Epub 2016 Oct 26. PMID:27783466<ref>PMID:27783466</ref>

-	~~Description: Structure~~ of ~~GH36 alpha-galactosidase from Thermotoga maritime in complex with intact cyclopropyl-carbasugar~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Pengelly, R~~]]	+	<div class="pdbe-citations 5m12" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Alpha-galactosidase]]
	[[Category: Gloster, T]]		[[Category: Gloster, T]]
		+	[[Category: Pengelly, R]]
		+	[[Category: Glycoside hydrolase]]
		+	[[Category: Hydrolase]]

OCA: Protected "5m12" [edit=sysop:move=sysop]

OCA — Wed, 19 Oct 2016 15:02:18 GMT

Protected "5m12" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:02, 19 October 2016

OCA: New page: '''Unreleased structure''' The entry 5m12 is ON HOLD Authors: Pengelly, R., Gloster, T. Description: Structure of GH36 alpha-galactosidase from Thermotoga maritime in complex with inta...

OCA — Wed, 19 Oct 2016 15:02:17 GMT

New page: '''Unreleased structure''' The entry 5m12 is ON HOLD Authors: Pengelly, R., Gloster, T. Description: Structure of GH36 alpha-galactosidase from Thermotoga maritime in complex with inta...

New page

'''Unreleased structure'''

The entry 5m12 is ON HOLD

Authors: Pengelly, R., Gloster, T.

Description: Structure of GH36 alpha-galactosidase from Thermotoga maritime in complex with intact cyclopropyl-carbasugar.
[[Category: Unreleased Structures]]
[[Category: Pengelly, R]]
[[Category: Gloster, T]]