5kd5 - Revision history

OCA at 09:58, 27 September 2023

2023-09-27T09:58:24Z

←Older revision		Revision as of 09:58, 27 September 2023
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	<StructureSection load='5kd5' size='340' side='right'caption='[[5kd5]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='5kd5' size='340' side='right'caption='[[5kd5]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kd5]] is a 1 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=5KD5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5KD5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kd5]] is a 1 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=5KD5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KD5 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDO:1,2~~-~~ETHANEDIOL'>EDO</scene>~~, ~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.65Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5kd2\|5kd2]]~~, ~~[[5kd8\|5kd8]], [[5kdj\|5kdj]], [[5kdn\|5kdn]], [[5kds\|5kds]], [[5kdu\|5kdu]], [[5kdv\|5kdv]], [[5kdw\|5kdw]], [[5kdx\|5kdx]]</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<~~tr id~~='~~gene~~'><~~td class="sblockLbl"~~><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">BT_4244 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226186 BACTN])~~</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=5kd5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kd5 OCA], [https://pdbe.org/5kd5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kd5 RCSB], [https://www.ebi.ac.uk/pdbsum/5kd5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kd5 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=5kd5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kd5 OCA], [~~http~~://pdbe.org/5kd5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kd5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kd5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kd5 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q89ZX7_BACTN Q89ZX7_BACTN]
	<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: ~~Bactn~~]]	+	[[Category: Bacteroides thetaiotaomicron VPI-5482]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Boraston~~, A B~~]]	+	[[Category: Boraston AB]]
-	[[Category: Noach, I]]	+	[[Category: Noach I]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: O-glycopeptidase]]~~	+
-	~~[[Category: Pf13402/m60-like~~]]	+

OCA at 15:22, 8 July 2020

2020-07-08T15:22:46Z

←Older revision		Revision as of 15:22, 8 July 2020
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	==BT_4244 metallopeptidase from Bacteroides thetaiotaomicron==		==BT_4244 metallopeptidase from Bacteroides thetaiotaomicron==
-	<StructureSection load='5kd5' size='340' side='right' caption='[[5kd5]], [[Resolution\|resolution]] 1.65Å' scene=''>	+	<StructureSection load='5kd5' size='340' side='right'caption='[[5kd5]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kd5]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KD5 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KD5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kd5]] is a 1 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=5KD5 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5KD5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kd2\|5kd2]], [[5kd8\|5kd8]], [[5kdj\|5kdj]], [[5kdn\|5kdn]], [[5kds\|5kds]], [[5kdu\|5kdu]], [[5kdv\|5kdv]], [[5kdw\|5kdw]], [[5kdx\|5kdx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kd2\|5kd2]], [[5kd8\|5kd8]], [[5kdj\|5kdj]], [[5kdn\|5kdn]], [[5kds\|5kds]], [[5kdu\|5kdu]], [[5kdv\|5kdv]], [[5kdw\|5kdw]], [[5kdx\|5kdx]]</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=5kd5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kd5 OCA], [http://pdbe.org/5kd5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kd5 RCSB], [http://www.ebi.ac.uk/pdbsum/5kd5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kd5 ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BT_4244 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226186 BACTN])</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=5kd5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kd5 OCA], [http://pdbe.org/5kd5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kd5 RCSB], [http://www.ebi.ac.uk/pdbsum/5kd5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kd5 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bactn]]
		+	[[Category: Large Structures]]
	[[Category: Boraston, A B]]		[[Category: Boraston, A B]]
	[[Category: Noach, I]]		[[Category: Noach, I]]

OCA at 10:49, 1 February 2017

2017-02-01T10:49:31Z

←Older revision		Revision as of 10:49, 1 February 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=5kd5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kd5 OCA], [http://pdbe.org/5kd5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kd5 RCSB], [http://www.ebi.ac.uk/pdbsum/5kd5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kd5 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=5kd5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kd5 OCA], [http://pdbe.org/5kd5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kd5 RCSB], [http://www.ebi.ac.uk/pdbsum/5kd5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kd5 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The vast majority of proteins are posttranslationally altered, with the addition of covalently linked sugars (glycosylation) being one of the most abundant modifications. However, despite the hydrolysis of protein peptide bonds by peptidases being a process essential to all life on Earth, the fundamental details of how peptidases accommodate posttranslational modifications, including glycosylation, has not been addressed. Through biochemical analyses and X-ray crystallographic structures we show that to hydrolyze their substrates, three structurally related metallopeptidases require the specific recognition of O-linked glycan modifications via carbohydrate-specific subsites immediately adjacent to their peptidase catalytic machinery. The three peptidases showed selectivity for different glycans, revealing protein-specific adaptations to particular glycan modifications, yet always cleaved the peptide bond immediately preceding the glycosylated residue. This insight builds upon the paradigm of how peptidases recognize substrates and provides a molecular understanding of glycoprotein degradation.
		+
		+	Recognition of protein-linked glycans as a determinant of peptidase activity.,Noach I, Ficko-Blean E, Pluvinage B, Stuart C, Jenkins ML, Brochu D, Buenbrazo N, Wakarchuk W, Burke JE, Gilbert M, Boraston AB Proc Natl Acad Sci U S A. 2017 Jan 17. pii: 201615141. doi:, 10.1073/pnas.1615141114. PMID:28096352<ref>PMID:28096352</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5kd5" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:29, 18 January 2017

2017-01-18T16:29:47Z

←Older revision		Revision as of 16:29, 18 January 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5kd5 is ~~ON HOLD until Paper Publication~~	+	==BT_4244 metallopeptidase from Bacteroides thetaiotaomicron==
-		+	<StructureSection load='5kd5' size='340' side='right' caption='[[5kd5]], [[Resolution\|resolution]] 1.65Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5kd5]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KD5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KD5 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kd2\|5kd2]], [[5kd8\|5kd8]], [[5kdj\|5kdj]], [[5kdn\|5kdn]], [[5kds\|5kds]], [[5kdu\|5kdu]], [[5kdv\|5kdv]], [[5kdw\|5kdw]], [[5kdx\|5kdx]]</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=5kd5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kd5 OCA], [http://pdbe.org/5kd5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kd5 RCSB], [http://www.ebi.ac.uk/pdbsum/5kd5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kd5 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Boraston, A B]]
		+	[[Category: Noach, I]]
		+	[[Category: Hydrolase]]
		+	[[Category: O-glycopeptidase]]
		+	[[Category: Pf13402/m60-like]]

OCA at 00:15, 13 July 2016

2016-07-13T00:15:37Z

←Older revision		Revision as of 00:15, 13 July 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5kd5 is ON HOLD	+	The entry 5kd5 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5kd5" [edit=sysop:move=sysop]

2016-06-20T13:45:59Z

Protected "5kd5" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:45, 20 June 2016

OCA: New page: '''Unreleased structure''' The entry 5kd5 is ON HOLD Authors: Description: Category: Unreleased Structures

2016-06-20T13:45:58Z

New page: '''Unreleased structure''' The entry 5kd5 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5kd5 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]