4d11 - Revision history

OCA at 12:19, 20 December 2023

OCA — Wed, 20 Dec 2023 12:19:04 GMT

←Older revision		Revision as of 12:19, 20 December 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4d11]] is a 11 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D11 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D11 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4d11]] is a 11 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D11 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D11 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BBK:2-(ACETYLAMINO)-2-DEOXY-5-THIO-ALPHA-D-GALACTOPYRANOSE'>BBK</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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]] 2.85Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BBK:2-(ACETYLAMINO)-2-DEOXY-5-THIO-ALPHA-D-GALACTOPYRANOSE'>BBK</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></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=4d11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d11 OCA], [https://pdbe.org/4d11 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d11 RCSB], [https://www.ebi.ac.uk/pdbsum/4d11 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d11 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=4d11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d11 OCA], [https://pdbe.org/4d11 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d11 RCSB], [https://www.ebi.ac.uk/pdbsum/4d11 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d11 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/GALT2_HUMAN GALT2_HUMAN]] Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. Has a broad spectrum of substrates for peptides such as EA2, Muc5AC, Muc1a, Muc1b. Probably involved in O-linked glycosylation of the immunoglobulin A1 (IgA1) hinge region.<ref>PMID:9295285</ref> <ref>PMID:12438318</ref>	+	[https://www.uniprot.org/uniprot/GALT2_HUMAN GALT2_HUMAN] Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. Has a broad spectrum of substrates for peptides such as EA2, Muc5AC, Muc1a, Muc1b. Probably involved in O-linked glycosylation of the immunoglobulin A1 (IgA1) hinge region.<ref>PMID:9295285</ref> <ref>PMID:12438318</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 07:42, 14 September 2022

OCA — Wed, 14 Sep 2022 07:42:13 GMT

←Older revision		Revision as of 07:42, 14 September 2022
Line 3:		Line 3:
	<StructureSection load='4d11' size='340' side='right'caption='[[4d11]], [[Resolution\|resolution]] 2.85Å' scene=''>		<StructureSection load='4d11' size='340' side='right'caption='[[4d11]], [[Resolution\|resolution]] 2.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4d11]] is a 11 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D11 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4D11 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4d11]] is a 11 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D11 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D11 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BBK:2-(ACETYLAMINO)-2-DEOXY-5-THIO-ALPHA-D-GALACTOPYRANOSE'>BBK</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BBK:2-(ACETYLAMINO)-2-DEOXY-5-THIO-ALPHA-D-GALACTOPYRANOSE'>BBK</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d0t\|4d0t]], [[4d0z\|4d0z]]~~</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=4d11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d11 OCA], [https://pdbe.org/4d11 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d11 RCSB], [https://www.ebi.ac.uk/pdbsum/4d11 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d11 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=4d11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d11 OCA], [~~http~~://pdbe.org/4d11 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4d11 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4d11 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4d11 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/GALT2_HUMAN GALT2_HUMAN]] Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. Has a broad spectrum of substrates for peptides such as EA2, Muc5AC, Muc1a, Muc1b. Probably involved in O-linked glycosylation of the immunoglobulin A1 (IgA1) hinge region.<ref>PMID:9295285</ref> <ref>PMID:12438318</ref>	+	[[https://www.uniprot.org/uniprot/GALT2_HUMAN GALT2_HUMAN]] Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. Has a broad spectrum of substrates for peptides such as EA2, Muc5AC, Muc1a, Muc1b. Probably involved in O-linked glycosylation of the immunoglobulin A1 (IgA1) hinge region.<ref>PMID:9295285</ref> <ref>PMID:12438318</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Clausen, H]]	+	[[Category: Clausen H]]
-	[[Category: Companon, I]]	+	[[Category: Companon I]]
-	[[Category: Corzana, F]]	+	[[Category: Corzana F]]
-	[[Category: Hurtado-Guerrero, R]]	+	[[Category: Hurtado-Guerrero R]]
-	[[Category: Iglesias-Fernandez, J]]	+	[[Category: Iglesias-Fernandez J]]
-	[[Category: Kong, Y]]	+	[[Category: Kong Y]]
-	[[Category: Lira-Navarrete, E]]	+	[[Category: Lira-Navarrete E]]
-	[[Category: Peregrina~~, J M~~]]	+	[[Category: Peregrina JM]]
-	[[Category: Pinto~~, B M~~]]	+	[[Category: Pinto BM]]
-	[[Category: Rovira, C]]	+	[[Category: Rovira C]]
-	[[Category: Vocadlo, D]]	+	[[Category: Vocadlo D]]
-	[[Category: Zandberg~~, W F]]~~	+	[[Category: Zandberg WF]]
-	~~[[Category: Acetamido group]]~~	+
-	~~[[Category: Bi-bi kinetic mechanism]]~~	+
-	~~[[Category: Qm/mm metadynamic]]~~	+
-	~~[[Category: Retaining galnac-t2]]~~	+
-	~~[[Category: Substrate specificity]]~~	+
-	~~[[Category: Substrate-guided sni-type reaction]]~~	+
-	~~[[Category: Transferase-peptide complex~~]]	+

OCA at 09:15, 20 March 2019

OCA — Wed, 20 Mar 2019 09:15:31 GMT

←Older revision		Revision as of 09:15, 20 March 2019
Line 1:		Line 1:

	==GalNAc-T2 crystal soaked with UDP-5SGalNAc, mEA2 peptide and manganese (Lower resolution dataset)==		==GalNAc-T2 crystal soaked with UDP-5SGalNAc, mEA2 peptide and manganese (Lower resolution dataset)==
-	<StructureSection load='4d11' size='340' side='right' caption='[[4d11]], [[Resolution\|resolution]] 2.85Å' scene=''>	+	<StructureSection load='4d11' size='340' side='right'caption='[[4d11]], [[Resolution\|resolution]] 2.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4d11]] is a 11 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D11 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D11 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4d11]] is a 11 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D11 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D11 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BBK:2-(ACETYLAMINO)-2-DEOXY-5-THIO-ALPHA-D-GALACTOPYRANOSE'>BBK</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BBK:2-(ACETYLAMINO)-2-DEOXY-5-THIO-ALPHA-D-GALACTOPYRANOSE'>BBK</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d0t\|4d0t]], [[4d0z\|4d0z]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d0t\|4d0t]], [[4d0z\|4d0z]]</td></tr>
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Clausen, H]]		[[Category: Clausen, H]]
	[[Category: Companon, I]]		[[Category: Companon, I]]

OCA at 20:27, 4 August 2016

OCA — Thu, 04 Aug 2016 20:27:08 GMT

←Older revision		Revision as of 20:27, 4 August 2016
Line 1:		Line 1:
		+
	==GalNAc-T2 crystal soaked with UDP-5SGalNAc, mEA2 peptide and manganese (Lower resolution dataset)==		==GalNAc-T2 crystal soaked with UDP-5SGalNAc, mEA2 peptide and manganese (Lower resolution dataset)==
	<StructureSection load='4d11' size='340' side='right' caption='[[4d11]], [[Resolution\|resolution]] 2.85Å' scene=''>		<StructureSection load='4d11' size='340' side='right' caption='[[4d11]], [[Resolution\|resolution]] 2.85Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BBK:2-(ACETYLAMINO)-2-DEOXY-5-THIO-ALPHA-D-GALACTOPYRANOSE'>BBK</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BBK:2-(ACETYLAMINO)-2-DEOXY-5-THIO-ALPHA-D-GALACTOPYRANOSE'>BBK</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d0t\|4d0t]], [[4d0z\|4d0z]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d0t\|4d0t]], [[4d0z\|4d0z]]</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=4d11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d11 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4d11 RCSB], [http://www.ebi.ac.uk/pdbsum/4d11 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=4d11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d11 OCA], [http://pdbe.org/4d11 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d11 RCSB], [http://www.ebi.ac.uk/pdbsum/4d11 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4d11 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	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 4d11" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:52, 25 December 2014

OCA — Thu, 25 Dec 2014 12:52:10 GMT

←Older revision		Revision as of 12:52, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4d11]] is a 11 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D11 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D11 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4d11]] is a 11 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D11 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D11 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BBK:2-(ACETYLAMINO)-2-DEOXY-5-THIO-ALPHA-D-GALACTOPYRANOSE'>BBK</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BBK:2-(ACETYLAMINO)-2-DEOXY-5-THIO-ALPHA-D-GALACTOPYRANOSE'>BBK</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d0t\|4d0t]], [[4d0z\|4d0z]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d0t\|4d0t]], [[4d0z\|4d0z]]</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=4d11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d11 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4d11 RCSB], [http://www.ebi.ac.uk/pdbsum/4d11 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=4d11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d11 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4d11 RCSB], [http://www.ebi.ac.uk/pdbsum/4d11 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GALT2_HUMAN GALT2_HUMAN]] Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. Has a broad spectrum of substrates for peptides such as EA2, Muc5AC, Muc1a, Muc1b. Probably involved in O-linked glycosylation of the immunoglobulin A1 (IgA1) hinge region.<ref>PMID:9295285</ref> <ref>PMID:12438318</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Clausen, H.]]	+	[[Category: Clausen, H]]
-	[[Category: Companon, I.]]	+	[[Category: Companon, I]]
-	[[Category: Corzana, F.]]	+	[[Category: Corzana, F]]
-	[[Category: Hurtado-Guerrero, R.]]	+	[[Category: Hurtado-Guerrero, R]]
-	[[Category: Iglesias-Fernandez, J.]]	+	[[Category: Iglesias-Fernandez, J]]
-	[[Category: Kong, Y.]]	+	[[Category: Kong, Y]]
-	[[Category: Lira-Navarrete, E.]]	+	[[Category: Lira-Navarrete, E]]
-	[[Category: Peregrina, J M.]]	+	[[Category: Peregrina, J M]]
-	[[Category: Pinto, B M.]]	+	[[Category: Pinto, B M]]
-	[[Category: Rovira, C.]]	+	[[Category: Rovira, C]]
-	[[Category: Vocadlo, D.]]	+	[[Category: Vocadlo, D]]
-	[[Category: Zandberg, W F.]]	+	[[Category: Zandberg, W F]]
	[[Category: Acetamido group]]		[[Category: Acetamido group]]
	[[Category: Bi-bi kinetic mechanism]]		[[Category: Bi-bi kinetic mechanism]]

OCA at 06:25, 2 July 2014

OCA — Wed, 02 Jul 2014 06:25:57 GMT

←Older revision		Revision as of 06:25, 2 July 2014
Line 7:		Line 7:
	<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=4d11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d11 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4d11 RCSB], [http://www.ebi.ac.uk/pdbsum/4d11 PDBsum]</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=4d11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d11 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4d11 RCSB], [http://www.ebi.ac.uk/pdbsum/4d11 PDBsum]</span></td></tr>
	<table>		<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The retaining glycosyltransferase GalNAc-T2 is a member of a large family of human polypeptide GalNAc-transferases that is responsible for the post-translational modification of many cell-surface proteins. By the use of combined structural and computational approaches, we provide the first set of structural snapshots of the enzyme during the catalytic cycle and combine these with quantum-mechanics/molecular-mechanics (QM/MM) metadynamics to unravel the catalytic mechanism of this retaining enzyme at the atomic-electronic level of detail. Our study provides a detailed structural rationale for an ordered bi-bi kinetic mechanism and reveals critical aspects of substrate recognition, which dictate the specificity for acceptor Thr versus Ser residues and enforce a front-face SN i-type reaction in which the substrate N-acetyl sugar substituent coordinates efficient glycosyl transfer.
		+
		+	Substrate-Guided Front-Face Reaction Revealed by Combined Structural Snapshots and Metadynamics for the Polypeptide N-Acetylgalactosaminyltransferase 2.,Lira-Navarrete E, Iglesias-Fernandez J, Zandberg WF, Companon I, Kong Y, Corzana F, Pinto BM, Clausen H, Peregrina JM, Vocadlo DJ, Rovira C, Hurtado-Guerrero R Angew Chem Int Ed Engl. 2014 Jun 20. doi: 10.1002/anie.201402781. PMID:24954443<ref>PMID:24954443</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:01, 28 May 2014

OCA — Wed, 28 May 2014 10:01:25 GMT

←Older revision		Revision as of 10:01, 28 May 2014
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==GalNAc-T2 crystal soaked with UDP-5SGalNAc, mEA2 peptide and manganese (Lower resolution dataset)==
-		+	<StructureSection load='4d11' size='340' side='right' caption='[[4d11]], [[Resolution\|resolution]] 2.85Å' scene=''>
-	~~The entry~~ 4d11 is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4d11]] is a 11 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D11 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D11 FirstGlance]. <br>
-	~~Authors~~: ~~Lira~~-~~Navarrete~~, E., ~~Iglesias~~-~~Fernandez~~, J., ~~Zandberg~~, W.F., ~~Companon, I~~., ~~Kong, Y~~., Corzana, F., ~~Pinto~~, ~~B.M~~., ~~Clausen, H~~., Peregrina, J.M., ~~Vocadlo, D~~., Rovira, C., ~~Hurtado-Guerrero~~, R.	+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BBK:2-(ACETYLAMINO)-2-DEOXY-5-THIO-ALPHA-D-GALACTOPYRANOSE'>BBK</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene><br>
-		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d0t\|4d0t]], [[4d0z\|4d0z]]</td></tr>
-	~~Description~~: ~~GalNAc~~-~~T2 soaked with UDP~~-~~5SGalNAc, mEA2~~ peptide ~~and manganese (Lower resolution dataset)~~	+	<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=4d11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d11 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4d11 RCSB], [http://www.ebi.ac.uk/pdbsum/4d11 PDBsum]</span></td></tr>
		+	<table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Clausen, H.]]
		+	[[Category: Companon, I.]]
		+	[[Category: Corzana, F.]]
		+	[[Category: Hurtado-Guerrero, R.]]
		+	[[Category: Iglesias-Fernandez, J.]]
		+	[[Category: Kong, Y.]]
		+	[[Category: Lira-Navarrete, E.]]
		+	[[Category: Peregrina, J M.]]
		+	[[Category: Pinto, B M.]]
		+	[[Category: Rovira, C.]]
		+	[[Category: Vocadlo, D.]]
		+	[[Category: Zandberg, W F.]]
		+	[[Category: Acetamido group]]
		+	[[Category: Bi-bi kinetic mechanism]]
		+	[[Category: Qm/mm metadynamic]]
		+	[[Category: Retaining galnac-t2]]
		+	[[Category: Substrate specificity]]
		+	[[Category: Substrate-guided sni-type reaction]]
		+	[[Category: Transferase-peptide complex]]

OCA at 07:02, 14 May 2014

OCA — Wed, 14 May 2014 07:02:10 GMT

←Older revision		Revision as of 07:02, 14 May 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4d11 is ON HOLD until ~~sometime in the future~~	+	The entry 4d11 is ON HOLD until Paper Publication

	Authors: Lira-Navarrete, E., Iglesias-Fernandez, J., Zandberg, W.F., Companon, I., Kong, Y., Corzana, F., Pinto, B.M., Clausen, H., Peregrina, J.M., Vocadlo, D., Rovira, C., Hurtado-Guerrero, R.		Authors: Lira-Navarrete, E., Iglesias-Fernandez, J., Zandberg, W.F., Companon, I., Kong, Y., Corzana, F., Pinto, B.M., Clausen, H., Peregrina, J.M., Vocadlo, D., Rovira, C., Hurtado-Guerrero, R.

	Description: GalNAc-T2 soaked with UDP-5SGalNAc, mEA2 peptide and manganese (Lower resolution dataset)		Description: GalNAc-T2 soaked with UDP-5SGalNAc, mEA2 peptide and manganese (Lower resolution dataset)

OCA: Protected "4d11" [edit=sysop:move=sysop]

OCA — Wed, 07 May 2014 07:24:50 GMT

Protected "4d11" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:24, 7 May 2014

OCA: New page: '''Unreleased structure''' The entry 4d11 is ON HOLD until sometime in the future Authors: Lira-Navarrete, E., Iglesias-Fernandez, J., Zandberg, W.F., Companon, I., Kong, Y., Corzana, F...

OCA — Wed, 07 May 2014 07:24:49 GMT

New page: '''Unreleased structure''' The entry 4d11 is ON HOLD until sometime in the future Authors: Lira-Navarrete, E., Iglesias-Fernandez, J., Zandberg, W.F., Companon, I., Kong, Y., Corzana, F...

New page

'''Unreleased structure'''

The entry 4d11 is ON HOLD until sometime in the future

Authors: Lira-Navarrete, E., Iglesias-Fernandez, J., Zandberg, W.F., Companon, I., Kong, Y., Corzana, F., Pinto, B.M., Clausen, H., Peregrina, J.M., Vocadlo, D., Rovira, C., Hurtado-Guerrero, R.

Description: GalNAc-T2 soaked with UDP-5SGalNAc, mEA2 peptide and manganese (Lower resolution dataset)