5d88 - Revision history

OCA at 11:46, 9 May 2024

2024-05-09T11:46:46Z

←Older revision		Revision as of 11:46, 9 May 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5d88]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanopyrus_kandleri Methanopyrus kandleri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D88 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D88 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5d88]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanopyrus_kandleri Methanopyrus kandleri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D88 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D88 FirstGlance]. <br>
-	</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=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]] 1.66Å</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=ZN:ZINC+ION'>ZN</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=5d88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d88 OCA], [https://pdbe.org/5d88 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d88 RCSB], [https://www.ebi.ac.uk/pdbsum/5d88 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d88 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=5d88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d88 OCA], [https://pdbe.org/5d88 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d88 RCSB], [https://www.ebi.ac.uk/pdbsum/5d88 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d88 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:25, 21 June 2023

2023-06-21T10:25:25Z

←Older revision		Revision as of 10:25, 21 June 2023
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	<StructureSection load='5d88' size='340' side='right'caption='[[5d88]], [[Resolution\|resolution]] 1.66Å' scene=''>		<StructureSection load='5d88' size='340' side='right'caption='[[5d88]], [[Resolution\|resolution]] 1.66Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5d88]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Dsm_6324 Dsm 6324~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D88 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5D88 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5d88]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanopyrus_kandleri Methanopyrus kandleri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D88 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D88 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=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=ACT:ACETATE+ION'>ACT</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">MK0906 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2320 DSM 6324])~~</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=5d88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d88 OCA], [https://pdbe.org/5d88 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d88 RCSB], [https://www.ebi.ac.uk/pdbsum/5d88 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d88 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=5d88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d88 OCA], [~~http~~://pdbe.org/5d88 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5d88 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5d88 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5d88 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8TWX5_METKA Q8TWX5_METKA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Dsm 6324]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Baumann, U~~]]	+	[[Category: Methanopyrus kandleri]]
-	[[Category: ~~Monatda, A A.M~~]]	+	[[Category: Baumann U]]
-	[[Category: ~~Schacherl, M~~]]	+	[[Category: Monatda AAM]]
-	[[Category: ~~Hydrolase]]~~	+	[[Category: Schacherl M]]
-	~~[[Category: Tim barrel]]~~	+
-	~~[[Category: U32 peptidase~~]]	+

OCA at 10:42, 1 April 2020

2020-04-01T10:42:39Z

←Older revision		Revision as of 10:42, 1 April 2020
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	==The Structure of the U32 Peptidase Mk0906==		==The Structure of the U32 Peptidase Mk0906==
-	<StructureSection load='5d88' size='340' side='right' caption='[[5d88]], [[Resolution\|resolution]] 1.66Å' scene=''>	+	<StructureSection load='5d88' size='340' side='right'caption='[[5d88]], [[Resolution\|resolution]] 1.66Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5d88]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D88 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D88 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5d88]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dsm_6324 Dsm 6324]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D88 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D88 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=ZN:ZINC+ION'>ZN</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=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MK0906 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2320 DSM 6324])</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=5d88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d88 OCA], [http://pdbe.org/5d88 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d88 RCSB], [http://www.ebi.ac.uk/pdbsum/5d88 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5d88 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=5d88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d88 OCA], [http://pdbe.org/5d88 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d88 RCSB], [http://www.ebi.ac.uk/pdbsum/5d88 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5d88 ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Dsm 6324]]
		+	[[Category: Large Structures]]
	[[Category: Baumann, U]]		[[Category: Baumann, U]]
	[[Category: Monatda, A A.M]]		[[Category: Monatda, A A.M]]

OCA at 06:36, 26 July 2016

2016-07-26T06:36:06Z

←Older revision		Revision as of 06:36, 26 July 2016
Line 1:		Line 1:
		+
	==The Structure of the U32 Peptidase Mk0906==		==The Structure of the U32 Peptidase Mk0906==
	<StructureSection load='5d88' size='340' side='right' caption='[[5d88]], [[Resolution\|resolution]] 1.66Å' scene=''>		<StructureSection load='5d88' size='340' side='right' caption='[[5d88]], [[Resolution\|resolution]] 1.66Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[5d88]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D88 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D88 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5d88]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D88 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D88 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=ZN:ZINC+ION'>ZN</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=ZN:ZINC+ION'>ZN</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=5d88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d88 OCA], [http://pdbe.org/5d88 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d88 RCSB], [http://www.ebi.ac.uk/pdbsum/5d88 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=5d88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d88 OCA], [http://pdbe.org/5d88 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d88 RCSB], [http://www.ebi.ac.uk/pdbsum/5d88 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5d88 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The U32 family is a collection of over 2500 annotated peptidases in the MEROPS database with unknown catalytic mechanism. They mainly occur in bacteria and archaea, but a few representatives have also been identified in eukarya. Many of the U32 members have been linked to pathogenicity, such as proteins from Helicobacter and Salmonella. The first crystal structure analysis of a U32 catalytic domain from Methanopyrus kandleri (gene mk0906) reveals a modified (betaalpha)8 TIM-barrel fold with some unique features. The connecting segment between strands beta7 and beta8 is extended and helix alpha7 is located on top of the C-terminal end of the barrel body. The protein exhibits a dimeric quaternary structure in which a zinc ion is symmetrically bound by histidine and cysteine side chains from both monomers. These residues reside in conserved sequence motifs. No typical proteolytic motifs are discernible in the three-dimensional structure, and biochemical assays failed to demonstrate proteolytic activity. A tunnel in which an acetate ion is bound is located in the C-terminal part of the beta-barrel. Two hydrophobic grooves lead to a tunnel at the C-terminal end of the barrel in which an acetate ion is bound. One of the grooves binds to a Strep-Tag II of another dimer in the crystal lattice. Thus, these grooves may be binding sites for hydrophobic peptides or other ligands.
		+
		+	The first crystal structure of the peptidase domain of the U32 peptidase family.,Schacherl M, Montada AA, Brunstein E, Baumann U Acta Crystallogr D Biol Crystallogr. 2015 Dec 1;71(Pt 12):2505-12. doi:, 10.1107/S1399004715019549. Epub 2015 Nov 27. PMID:26627657<ref>PMID:26627657</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5d88" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:17, 2 December 2015

2015-12-02T16:17:21Z

←Older revision		Revision as of 16:17, 2 December 2015
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==The Structure of the U32 Peptidase Mk0906==
-		+	<StructureSection load='5d88' size='340' side='right' caption='[[5d88]], [[Resolution\|resolution]] 1.66Å' scene=''>
-	~~The entry~~ 5d88 is ~~ON HOLD~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5d88]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D88 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D88 FirstGlance]. <br>
-	~~Authors~~: ~~Baumann, U~~.~~, Schacherl, M~~.~~, Monatda, A~~.A.M.	+	</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=ZN:ZINC+ION'>ZN</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=5d88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d88 OCA], [http://pdbe.org/5d88 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d88 RCSB], [http://www.ebi.ac.uk/pdbsum/5d88 PDBsum]</span></td></tr>
-	~~Description:~~	+	</table>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	__TOC__
-	[[~~Category~~: ~~Monatda~~, A.A.M]]	+	</StructureSection>
	[[Category: Baumann, U]]		[[Category: Baumann, U]]
		+	[[Category: Monatda, A A.M]]
	[[Category: Schacherl, M]]		[[Category: Schacherl, M]]
		+	[[Category: Hydrolase]]
		+	[[Category: Tim barrel]]
		+	[[Category: U32 peptidase]]

OCA: Protected "5d88" [edit=sysop:move=sysop]

2015-08-26T12:32:13Z

Protected "5d88" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:32, 26 August 2015

OCA: New page: '''Unreleased structure''' The entry 5d88 is ON HOLD Authors: Baumann, U., Schacherl, M., Monatda, A.A.M. Description: Category: Unreleased Structures Category: Monatda, A.A.M...

2015-08-26T12:32:11Z

New page: '''Unreleased structure''' The entry 5d88 is ON HOLD Authors: Baumann, U., Schacherl, M., Monatda, A.A.M. Description: Category: Unreleased Structures Category: Monatda, A.A.M...

New page

'''Unreleased structure'''

The entry 5d88 is ON HOLD

Authors: Baumann, U., Schacherl, M., Monatda, A.A.M.

Description:
[[Category: Unreleased Structures]]
[[Category: Monatda, A.A.M]]
[[Category: Baumann, U]]
[[Category: Schacherl, M]]