6hmh - Revision history

OCA at 11:32, 24 January 2024

2024-01-24T11:32:59Z

←Older revision		Revision as of 11:32, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6hmh' size='340' side='right'caption='[[6hmh]], [[Resolution\|resolution]] 1.03Å' scene=''>		<StructureSection load='6hmh' size='340' side='right'caption='[[6hmh]], [[Resolution\|resolution]] 1.03Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6hmh]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bacteroides_sp._xb1a~~ Bacteroides ~~sp. xb1a~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HMH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6HMH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6hmh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_xylanisolvens_XB1A Bacteroides xylanisolvens XB1A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HMH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6HMH FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GDQ:(1~{S},2~{R},3~{R},4~{R},6~{S})-4-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3-diol'>GDQ</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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]] 1.03Å</td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">BXY_34140 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=657309 Bacteroides sp. XB1A])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GDQ:(1~{S},2~{R},3~{R},4~{R},6~{S})-4-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3-diol'>GDQ</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=PRD_900111:2alpha-alpha-mannobiose'>PRD_900111</scene></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=6hmh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hmh OCA], [~~http~~://pdbe.org/6hmh PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6hmh RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6hmh PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6hmh 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=6hmh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hmh OCA], [https://pdbe.org/6hmh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6hmh RCSB], [https://www.ebi.ac.uk/pdbsum/6hmh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6hmh ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D6D1V7_9BACE D6D1V7_9BACE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacteroides ~~sp. xb1a~~]]	+	[[Category: Bacteroides xylanisolvens XB1A]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bernardo-Seisdedos, G]]	+	[[Category: Bernardo-Seisdedos G]]
-	[[Category: Davies~~, G J~~]]	+	[[Category: Davies GJ]]
-	[[Category: Jimenez-Barbero, J]]	+	[[Category: Jimenez-Barbero J]]
-	[[Category: Lu, D]]	+	[[Category: Lu D]]
-	[[Category: Millet, O]]	+	[[Category: Millet O]]
-	[[Category: Sobala~~, L F~~]]	+	[[Category: Sobala LF]]
-	[[Category: Sollogoub, M]]	+	[[Category: Sollogoub M]]
-	[[Category: Zhang, Y]]	+	[[Category: Zhang Y]]
-	[[Category: Zhu, S]]	+	[[Category: Zhu S]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 07:57, 24 April 2019

2019-04-24T07:57:48Z

←Older revision		Revision as of 07:57, 24 April 2019
Line 1:		Line 1:

	==Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with alpha-Glc-1,3-(1,2-anhydro-carba-glucosamine) and alpha-1,2-mannobiose==		==Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with alpha-Glc-1,3-(1,2-anhydro-carba-glucosamine) and alpha-1,2-mannobiose==
-	<StructureSection load='6hmh' size='340' side='right' caption='[[6hmh]], [[Resolution\|resolution]] 1.03Å' scene=''>	+	<StructureSection load='6hmh' size='340' side='right'caption='[[6hmh]], [[Resolution\|resolution]] 1.03Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6hmh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_sp._xb1a Bacteroides sp. xb1a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HMH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HMH FirstGlance]. <br>		<table><tr><td colspan='2'>[[6hmh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_sp._xb1a Bacteroides sp. xb1a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HMH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HMH FirstGlance]. <br>
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Bacteroides sp. xb1a]]		[[Category: Bacteroides sp. xb1a]]
		+	[[Category: Large Structures]]
	[[Category: Bernardo-Seisdedos, G]]		[[Category: Bernardo-Seisdedos, G]]
	[[Category: Davies, G J]]		[[Category: Davies, G J]]

OCA at 21:05, 2 December 2018

2018-12-02T21:05:28Z

←Older revision		Revision as of 21:05, 2 December 2018
Line 3:		Line 3:
	<StructureSection load='6hmh' size='340' side='right' caption='[[6hmh]], [[Resolution\|resolution]] 1.03Å' scene=''>		<StructureSection load='6hmh' size='340' side='right' caption='[[6hmh]], [[Resolution\|resolution]] 1.03Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6hmh]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HMH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HMH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6hmh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_sp._xb1a Bacteroides sp. xb1a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HMH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HMH FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GDQ:(1~{S},2~{R},3~{R},4~{R},6~{S})-4-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3-diol'>GDQ</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GDQ:(1~{S},2~{R},3~{R},4~{R},6~{S})-4-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3-diol'>GDQ</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BXY_34140 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=657309 Bacteroides sp. XB1A])</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=6hmh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hmh OCA], [http://pdbe.org/6hmh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hmh RCSB], [http://www.ebi.ac.uk/pdbsum/6hmh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hmh 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=6hmh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hmh OCA], [http://pdbe.org/6hmh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hmh RCSB], [http://www.ebi.ac.uk/pdbsum/6hmh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hmh ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Understanding the enzyme reaction mechanism can lead to the design of enzyme inhibitors. A Claisen rearrangement was used to allow conversion of an alpha-1,4-disaccharide into an alpha-1,3-linked glycosyl carbasugar to target the endo-alpha-mannosidase from the GH99 glycosidase family, which, unusually, is believed to act through a 1,2-anhydrosugar "epoxide" intermediate. Using NMR and X-ray crystallography, it is shown that glucosyl carbasugar alpha-aziridines can act as reasonably potent endo-alpha-mannosidase inhibitors, likely by virtue of their shape mimicry and the interactions of the aziridine nitrogen with the conserved catalytic acid/base of the enzyme active site.
		+
		+	From 1,4-Disaccharide to 1,3-Glycosyl Carbasugar: Synthesis of a Bespoke Inhibitor of Family GH99 Endo-alpha-mannosidase.,Lu D, Zhu S, Sobala LF, Bernardo-Seisdedos G, Millet O, Zhang Y, Jimenez-Barbero J, Davies GJ, Sollogoub M Org Lett. 2018 Nov 14. doi: 10.1021/acs.orglett.8b03260. PMID:30427198<ref>PMID:30427198</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6hmh" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacteroides sp. xb1a]]
	[[Category: Bernardo-Seisdedos, G]]		[[Category: Bernardo-Seisdedos, G]]
	[[Category: Davies, G J]]		[[Category: Davies, G J]]

OCA at 08:22, 26 September 2018

2018-09-26T08:22:29Z

←Older revision		Revision as of 08:22, 26 September 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6hmh is ON HOLD~~	+	==Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with alpha-Glc-1,3-(1,2-anhydro-carba-glucosamine) and alpha-1,2-mannobiose==
-		+	<StructureSection load='6hmh' size='340' side='right' caption='[[6hmh]], [[Resolution\|resolution]] 1.03Å' scene=''>
-	~~Authors: Sobala, L.F., Lu, D., Zhu, S., Bernardo-Seisdedos, G., Millet, O., Zhang, Y., Sollogoub, M., Jimenez-Barbero, J., Davies, G.J.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6hmh]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HMH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HMH FirstGlance]. <br>
-	~~Description:~~ Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with alpha-Glc-1,3-(1,2-anhydro-carba-glucosamine) and alpha-1,2-mannobiose	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GDQ:(1~{S},2~{R},3~{R},4~{R},6~{S})-4-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3-diol'>GDQ</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=6hmh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hmh OCA], [http://pdbe.org/6hmh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hmh RCSB], [http://www.ebi.ac.uk/pdbsum/6hmh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hmh ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bernardo-Seisdedos, G]]
		+	[[Category: Davies, G J]]
		+	[[Category: Jimenez-Barbero, J]]
		+	[[Category: Lu, D]]
	[[Category: Millet, O]]		[[Category: Millet, O]]
-	[[Category: ~~Jimenez-Barbero~~, J]]	+	[[Category: Sobala, L F]]
	[[Category: Sollogoub, M]]		[[Category: Sollogoub, M]]
	[[Category: Zhang, Y]]		[[Category: Zhang, Y]]
-	[[Category: Lu, D]]
-	[[Category: Davies, G.J]]
-	[[Category: Bernardo-Seisdedos, G]]
-	[[Category: Sobala, L.F]]
	[[Category: Zhu, S]]		[[Category: Zhu, S]]
		+	[[Category: Hydrolase]]

OCA: Protected "6hmh" [edit=sysop:move=sysop]

2018-09-19T18:13:54Z

Protected "6hmh" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:13, 19 September 2018

OCA: New page: '''Unreleased structure''' The entry 6hmh is ON HOLD Authors: Sobala, L.F., Lu, D., Zhu, S., Bernardo-Seisdedos, G., Millet, O., Zhang, Y., Sollogoub, M., Jimenez-Barbero, J., Davies, G...

2018-09-19T18:13:52Z

New page: '''Unreleased structure''' The entry 6hmh is ON HOLD Authors: Sobala, L.F., Lu, D., Zhu, S., Bernardo-Seisdedos, G., Millet, O., Zhang, Y., Sollogoub, M., Jimenez-Barbero, J., Davies, G...

New page

'''Unreleased structure'''

The entry 6hmh is ON HOLD

Authors: Sobala, L.F., Lu, D., Zhu, S., Bernardo-Seisdedos, G., Millet, O., Zhang, Y., Sollogoub, M., Jimenez-Barbero, J., Davies, G.J.

Description: Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with alpha-Glc-1,3-(1,2-anhydro-carba-glucosamine) and alpha-1,2-mannobiose
[[Category: Unreleased Structures]]
[[Category: Millet, O]]
[[Category: Jimenez-Barbero, J]]
[[Category: Sollogoub, M]]
[[Category: Zhang, Y]]
[[Category: Lu, D]]
[[Category: Davies, G.J]]
[[Category: Bernardo-Seisdedos, G]]
[[Category: Sobala, L.F]]
[[Category: Zhu, S]]