5bwl - Revision history

OCA at 16:05, 8 November 2023

OCA — Wed, 08 Nov 2023 16:05:29 GMT

←Older revision		Revision as of 16:05, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5bwl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BWL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BWL FirstGlance]. <br>		<table><tr><td colspan='2'>[[5bwl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BWL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BWL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MCM:7-AMINO-4-METHYL-CHROMEN-2-ONE'>MCM</scene>, <scene name='pdbligand=SLL:(2S)-2-AZANYL-6-[(4-HYDROXY-4-OXO-BUTANOYL)AMINO]HEXANOIC+ACID'>SLL</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]] 1.548Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MCM:7-AMINO-4-METHYL-CHROMEN-2-ONE'>MCM</scene>, <scene name='pdbligand=SLL:(2S)-2-AZANYL-6-[(4-HYDROXY-4-OXO-BUTANOYL)AMINO]HEXANOIC+ACID'>SLL</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=5bwl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bwl OCA], [https://pdbe.org/5bwl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bwl RCSB], [https://www.ebi.ac.uk/pdbsum/5bwl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bwl 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=5bwl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bwl OCA], [https://pdbe.org/5bwl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bwl RCSB], [https://www.ebi.ac.uk/pdbsum/5bwl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bwl ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:11, 7 June 2023

OCA — Wed, 07 Jun 2023 06:11:13 GMT

←Older revision		Revision as of 06:11, 7 June 2023
Line 3:		Line 3:
	<StructureSection load='5bwl' size='340' side='right'caption='[[5bwl]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='5bwl' size='340' side='right'caption='[[5bwl]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5bwl]] is a 2 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=5BWL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5BWL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5bwl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BWL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BWL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MCM:7-AMINO-4-METHYL-CHROMEN-2-ONE'>MCM</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=MCM:7-AMINO-4-METHYL-CHROMEN-2-ONE'>MCM</scene>, <scene name='pdbligand=SLL:(2S)-2-AZANYL-6-[(4-HYDROXY-4-OXO-BUTANOYL)AMINO]HEXANOIC+ACID'>SLL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=SLL:(2S)-2-AZANYL-6-[(4-HYDROXY-4-OXO-BUTANOYL)AMINO]HEXANOIC+ACID'>SLL</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=5bwl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bwl OCA], [https://pdbe.org/5bwl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bwl RCSB], [https://www.ebi.ac.uk/pdbsum/5bwl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bwl ProSAT]</span></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat">[[5bwn\|5bwn]], [[5bwo\|5bwo]], [[5bwp\|5bwp]], [[5bwq\|5bwq]]</td></tr>~~	+
-	~~<tr id='gene~~'>~~<td class="sblockLbl"><b>[[Gene\|Gene:]]~~</b>~~</td><td class="sblockDat">SIRT5, SIR2L5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=5bwl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bwl OCA], [~~http~~://pdbe.org/5bwl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5bwl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5bwl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5bwl ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SIR5_HUMAN SIR5_HUMAN]] NAD-dependent lysine demalonylase and desuccinylase that specifically removes malonyl and succinyl groups on target proteins. Activates CPS1 and contributes to the regulation of blood ammonia levels during prolonged fasting: acts by mediating desuccinylation of CPS1, thereby increasing CPS1 activity in response to elevated NAD levels during fasting. Activates SOD1 by mediating its desuccinylation, leading to reduced reactive oxygen species. Has weak NAD-dependent protein deacetylase activity; however this activity may not be physiologically relevant in vivo. Can deacetylate cytochrome c (CYCS) and a number of other proteins in vitro.<ref>PMID:18680753</ref> <ref>PMID:21908771</ref> <ref>PMID:24140062</ref> <ref>PMID:22076378</ref>	+	[https://www.uniprot.org/uniprot/SIR5_HUMAN SIR5_HUMAN] NAD-dependent lysine demalonylase and desuccinylase that specifically removes malonyl and succinyl groups on target proteins. Activates CPS1 and contributes to the regulation of blood ammonia levels during prolonged fasting: acts by mediating desuccinylation of CPS1, thereby increasing CPS1 activity in response to elevated NAD levels during fasting. Activates SOD1 by mediating its desuccinylation, leading to reduced reactive oxygen species. Has weak NAD-dependent protein deacetylase activity; however this activity may not be physiologically relevant in vivo. Can deacetylate cytochrome c (CYCS) and a number of other proteins in vitro.<ref>PMID:18680753</ref> <ref>PMID:21908771</ref> <ref>PMID:24140062</ref> <ref>PMID:22076378</ref>

	==See Also==		==See Also==
Line 19:		Line 16:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Gai, W~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Jiang, H~~]]	+	[[Category: Gai W]]
-	[[Category: ~~Liu, D~~]]	+	[[Category: Jiang H]]
-	[[Category: ~~Hydrolase~~]]	+	[[Category: Liu D]]

OCA at 11:02, 18 March 2020

OCA — Wed, 18 Mar 2020 11:02:41 GMT

←Older revision		Revision as of 11:02, 18 March 2020
Line 1:		Line 1:

	==Crystal Structure of SIRT5 in Complex with a Coumarin-Labelled Succinyl Peptide==		==Crystal Structure of SIRT5 in Complex with a Coumarin-Labelled Succinyl Peptide==
-	<StructureSection load='5bwl' size='340' side='right' caption='[[5bwl]], [[Resolution\|resolution]] 1.55Å' scene=''>	+	<StructureSection load='5bwl' size='340' side='right'caption='[[5bwl]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5bwl]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BWL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BWL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5bwl]] is a 2 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=5BWL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BWL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MCM:7-AMINO-4-METHYL-CHROMEN-2-ONE'>MCM</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=MCM:7-AMINO-4-METHYL-CHROMEN-2-ONE'>MCM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SLL:(2S)-2-AZANYL-6-[(4-HYDROXY-4-OXO-BUTANOYL)AMINO]HEXANOIC+ACID'>SLL</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SLL:(2S)-2-AZANYL-6-[(4-HYDROXY-4-OXO-BUTANOYL)AMINO]HEXANOIC+ACID'>SLL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5bwn\|5bwn]], [[5bwo\|5bwo]], [[5bwp\|5bwp]], [[5bwq\|5bwq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5bwn\|5bwn]], [[5bwo\|5bwo]], [[5bwp\|5bwp]], [[5bwq\|5bwq]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SIRT5, SIR2L5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5bwl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bwl OCA], [http://pdbe.org/5bwl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bwl RCSB], [http://www.ebi.ac.uk/pdbsum/5bwl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bwl 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=5bwl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bwl OCA], [http://pdbe.org/5bwl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bwl RCSB], [http://www.ebi.ac.uk/pdbsum/5bwl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bwl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/SIR5_HUMAN SIR5_HUMAN]] NAD-dependent lysine demalonylase and desuccinylase that specifically removes malonyl and succinyl groups on target proteins. Activates CPS1 and contributes to the regulation of blood ammonia levels during prolonged fasting: acts by mediating desuccinylation of CPS1, thereby increasing CPS1 activity in response to elevated NAD levels during fasting. Activates SOD1 by mediating its desuccinylation, leading to reduced reactive oxygen species. Has weak NAD-dependent protein deacetylase activity; however this activity may not be physiologically relevant in vivo. Can deacetylate cytochrome c (CYCS) and a number of other proteins in vitro.<ref>PMID:18680753</ref> <ref>PMID:21908771</ref> <ref>PMID:24140062</ref> <ref>PMID:22076378</ref>		[[http://www.uniprot.org/uniprot/SIR5_HUMAN SIR5_HUMAN]] NAD-dependent lysine demalonylase and desuccinylase that specifically removes malonyl and succinyl groups on target proteins. Activates CPS1 and contributes to the regulation of blood ammonia levels during prolonged fasting: acts by mediating desuccinylation of CPS1, thereby increasing CPS1 activity in response to elevated NAD levels during fasting. Activates SOD1 by mediating its desuccinylation, leading to reduced reactive oxygen species. Has weak NAD-dependent protein deacetylase activity; however this activity may not be physiologically relevant in vivo. Can deacetylate cytochrome c (CYCS) and a number of other proteins in vitro.<ref>PMID:18680753</ref> <ref>PMID:21908771</ref> <ref>PMID:24140062</ref> <ref>PMID:22076378</ref>
		+
		+	==See Also==
		+	*[[Histone deacetylase 3D structures\|Histone deacetylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Gai, W]]		[[Category: Gai, W]]
	[[Category: Jiang, H]]		[[Category: Jiang, H]]
	[[Category: Liu, D]]		[[Category: Liu, D]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 11:41, 14 July 2016

OCA — Thu, 14 Jul 2016 11:41:35 GMT

←Older revision		Revision as of 11:41, 14 July 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5bwl is ON HOLD until Paper Publication~~	+	==Crystal Structure of SIRT5 in Complex with a Coumarin-Labelled Succinyl Peptide==
-		+	<StructureSection load='5bwl' size='340' side='right' caption='[[5bwl]], [[Resolution\|resolution]] 1.55Å' scene=''>
-	~~Authors: Gai, W., Jiang, H., Liu, D.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5bwl]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BWL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BWL FirstGlance]. <br>
-	~~Description:~~ Crystal Structure of SIRT5 in Complex with a Coumarin-Labelled Succinyl Peptide	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MCM:7-AMINO-4-METHYL-CHROMEN-2-ONE'>MCM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SLL:(2S)-2-AZANYL-6-[(4-HYDROXY-4-OXO-BUTANOYL)AMINO]HEXANOIC+ACID'>SLL</scene></td></tr>
-	[[~~Category~~: ~~Liu~~, D]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5bwn\|5bwn]], [[5bwo\|5bwo]], [[5bwp\|5bwp]], [[5bwq\|5bwq]]</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=5bwl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bwl OCA], [http://pdbe.org/5bwl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bwl RCSB], [http://www.ebi.ac.uk/pdbsum/5bwl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bwl ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SIR5_HUMAN SIR5_HUMAN]] NAD-dependent lysine demalonylase and desuccinylase that specifically removes malonyl and succinyl groups on target proteins. Activates CPS1 and contributes to the regulation of blood ammonia levels during prolonged fasting: acts by mediating desuccinylation of CPS1, thereby increasing CPS1 activity in response to elevated NAD levels during fasting. Activates SOD1 by mediating its desuccinylation, leading to reduced reactive oxygen species. Has weak NAD-dependent protein deacetylase activity; however this activity may not be physiologically relevant in vivo. Can deacetylate cytochrome c (CYCS) and a number of other proteins in vitro.<ref>PMID:18680753</ref> <ref>PMID:21908771</ref> <ref>PMID:24140062</ref> <ref>PMID:22076378</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Gai, W]]		[[Category: Gai, W]]
	[[Category: Jiang, H]]		[[Category: Jiang, H]]
		+	[[Category: Liu, D]]
		+	[[Category: Hydrolase]]

OCA at 10:54, 1 July 2015

OCA — Wed, 01 Jul 2015 10:54:02 GMT

←Older revision		Revision as of 10:54, 1 July 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Gai, W., Jiang, H., Liu, D.		Authors: Gai, W., Jiang, H., Liu, D.

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

OCA — Wed, 17 Jun 2015 13:59:44 GMT

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

←Older revision

Revision as of 13:59, 17 June 2015

OCA: New page: '''Unreleased structure''' The entry 5bwl is ON HOLD Authors: Gai, W., Jiang, H., Liu, D. Description: Crystal Structure of SIRT5 in Complex with a Coumarin-Labelled Succinyl Peptide [...

OCA — Wed, 17 Jun 2015 13:59:42 GMT

New page: '''Unreleased structure''' The entry 5bwl is ON HOLD Authors: Gai, W., Jiang, H., Liu, D. Description: Crystal Structure of SIRT5 in Complex with a Coumarin-Labelled Succinyl Peptide [...

New page

'''Unreleased structure'''

The entry 5bwl is ON HOLD

Authors: Gai, W., Jiang, H., Liu, D.

Description: Crystal Structure of SIRT5 in Complex with a Coumarin-Labelled Succinyl Peptide
[[Category: Unreleased Structures]]
[[Category: Liu, D]]
[[Category: Gai, W]]
[[Category: Jiang, H]]