2pbk - Revision history

OCA at 10:58, 30 August 2023

OCA — Wed, 30 Aug 2023 10:58:32 GMT

←Older revision		Revision as of 10:58, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2pbk' size='340' side='right'caption='[[2pbk]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='2pbk' size='340' side='right'caption='[[2pbk]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pbk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Hhv-8 Hhv-~~8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PBK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PBK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pbk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_gammaherpesvirus_8 Human gammaherpesvirus 8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PBK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PBK 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>~~</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]] 1.73Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=GG7:[(1R)-1-AMINOETHYL]PHOSPHONIC+ACID'>GG7</scene>, <scene name='pdbligand=TBG:3-METHYL-L-VALINE'>TBG</scene>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GG7:[(1R)-1-AMINOETHYL]PHOSPHONIC+ACID'>GG7</scene>, <scene name='pdbligand=TBG:3-METHYL-L-VALINE'>TBG</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1fl1\|1fl1]]</div></td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF010430 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37296 HHV-8])~~</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=2pbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pbk OCA], [https://pdbe.org/2pbk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pbk RCSB], [https://www.ebi.ac.uk/pdbsum/2pbk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pbk 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=2pbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pbk OCA], [https://pdbe.org/2pbk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pbk RCSB], [https://www.ebi.ac.uk/pdbsum/2pbk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pbk ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O36607_HHV8 O36607_HHV8]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Hhv-~~8]]	+	[[Category: Human gammaherpesvirus 8]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Goetz~~, D H~~]]	+	[[Category: Goetz DH]]
-	[[Category: Lazic, A]]	+	[[Category: Lazic A]]
-	~~[[Category: Herpesvirus protease]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex]]~~	+
-	~~[[Category: Kshv]]~~	+
-	~~[[Category: Kshv protease]]~~	+
-	~~[[Category: Viral protease]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 15:20, 17 June 2021

OCA — Thu, 17 Jun 2021 15:20:37 GMT

←Older revision		Revision as of 15:20, 17 June 2021
Line 1:		Line 1:

	==Crystal structure of KSHV protease in complex with hexapeptide phosphonate inhibitor==		==Crystal structure of KSHV protease in complex with hexapeptide phosphonate inhibitor==
-	<StructureSection load='2pbk' size='340' side='right' caption='[[2pbk]], [[Resolution\|resolution]] 1.73Å' scene=''>	+	<StructureSection load='2pbk' size='340' side='right'caption='[[2pbk]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pbk]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Hhv-8 Hhv-8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PBK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2PBK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pbk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Hhv-8 Hhv-8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PBK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PBK 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></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></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=GG7:[(1R)-1-AMINOETHYL]PHOSPHONIC+ACID'>GG7</scene>, <scene name='pdbligand=TBG:3-METHYL-L-VALINE'>TBG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=GG7:[(1R)-1-AMINOETHYL]PHOSPHONIC+ACID'>GG7</scene>, <scene name='pdbligand=TBG:3-METHYL-L-VALINE'>TBG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fl1\|1fl1]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1fl1\|1fl1]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF010430 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37296 HHV-8])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF010430 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37296 HHV-8])</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=2pbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pbk OCA], [~~http~~://pdbe.org/2pbk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2pbk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2pbk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2pbk 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=2pbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pbk OCA], [https://pdbe.org/2pbk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pbk RCSB], [https://www.ebi.ac.uk/pdbsum/2pbk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pbk ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Hhv-8]]		[[Category: Hhv-8]]
		+	[[Category: Large Structures]]
	[[Category: Goetz, D H]]		[[Category: Goetz, D H]]
	[[Category: Lazic, A]]		[[Category: Lazic, A]]

OCA at 08:48, 29 August 2018

OCA — Wed, 29 Aug 2018 08:48:25 GMT

←Older revision		Revision as of 08:48, 29 August 2018
Line 1:		Line 1:
		+
	==Crystal structure of KSHV protease in complex with hexapeptide phosphonate inhibitor==		==Crystal structure of KSHV protease in complex with hexapeptide phosphonate inhibitor==
	<StructureSection load='2pbk' size='340' side='right' caption='[[2pbk]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='2pbk' size='340' side='right' caption='[[2pbk]], [[Resolution\|resolution]] 1.73Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fl1\|1fl1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fl1\|1fl1]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF010430 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37296 HHV-8])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF010430 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37296 HHV-8])</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=2pbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pbk OCA], [http://pdbe.org/2pbk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pbk RCSB], [http://www.ebi.ac.uk/pdbsum/2pbk 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=2pbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pbk OCA], [http://pdbe.org/2pbk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pbk RCSB], [http://www.ebi.ac.uk/pdbsum/2pbk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pbk ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pb/2pbk_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pb/2pbk_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2pbk ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 11:34, 11 September 2015

OCA — Fri, 11 Sep 2015 11:34:30 GMT

←Older revision		Revision as of 11:34, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2pbk' size='340' side='right' caption='[[2pbk]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='2pbk' size='340' side='right' caption='[[2pbk]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pbk]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Human_herpesvirus_8 Human herpesvirus~~ 8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PBK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PBK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pbk]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Hhv-8 Hhv-8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PBK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PBK 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></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></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=GG7:[(1R)-1-AMINOETHYL]PHOSPHONIC+ACID'>GG7</scene>, <scene name='pdbligand=TBG:3-METHYL-L-VALINE'>TBG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=GG7:[(1R)-1-AMINOETHYL]PHOSPHONIC+ACID'>GG7</scene>, <scene name='pdbligand=TBG:3-METHYL-L-VALINE'>TBG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fl1\|1fl1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fl1\|1fl1]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF010430 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37296 ~~Human herpesvirus~~ 8])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF010430 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37296 HHV-8])</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=2pbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pbk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pbk RCSB], [http://www.ebi.ac.uk/pdbsum/2pbk 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=2pbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pbk OCA], [http://pdbe.org/2pbk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pbk RCSB], [http://www.ebi.ac.uk/pdbsum/2pbk PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		Line 27:
	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 2pbk" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human herpesvirus~~ 8]]	+	[[Category: Hhv-8]]
	[[Category: Goetz, D H]]		[[Category: Goetz, D H]]
	[[Category: Lazic, A]]		[[Category: Lazic, A]]

OCA at 15:47, 19 January 2015

OCA — Mon, 19 Jan 2015 15:47:02 GMT

←Older revision		Revision as of 15:47, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pbk]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_herpesvirus_8 Human herpesvirus 8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PBK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PBK FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pbk]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_herpesvirus_8 Human herpesvirus 8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PBK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PBK FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene><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></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=GG7:[(1R)-1-AMINOETHYL]PHOSPHONIC+ACID'>GG7</scene>, <scene name='pdbligand=TBG:3-METHYL-L-VALINE'>TBG</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=GG7:[(1R)-1-AMINOETHYL]PHOSPHONIC+ACID'>GG7</scene>, <scene name='pdbligand=TBG:3-METHYL-L-VALINE'>TBG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fl1\|1fl1]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fl1\|1fl1]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF010430 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37296 Human herpesvirus 8])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF010430 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37296 Human herpesvirus 8])</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=2pbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pbk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pbk RCSB], [http://www.ebi.ac.uk/pdbsum/2pbk 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=2pbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pbk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pbk RCSB], [http://www.ebi.ac.uk/pdbsum/2pbk PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Human herpesvirus 8]]		[[Category: Human herpesvirus 8]]
-	[[Category: Goetz, D H.]]	+	[[Category: Goetz, D H]]
-	[[Category: Lazic, A.]]	+	[[Category: Lazic, A]]
	[[Category: Herpesvirus protease]]		[[Category: Herpesvirus protease]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 18:56, 30 September 2014

OCA — Tue, 30 Sep 2014 18:56:47 GMT

←Older revision		Revision as of 18:56, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2pbk.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of KSHV protease in complex with hexapeptide phosphonate inhibitor==
		+	<StructureSection load='2pbk' size='340' side='right' caption='[[2pbk]], [[Resolution\|resolution]] 1.73Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2pbk]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_herpesvirus_8 Human herpesvirus 8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PBK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PBK FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=GG7:[(1R)-1-AMINOETHYL]PHOSPHONIC+ACID'>GG7</scene>, <scene name='pdbligand=TBG:3-METHYL-L-VALINE'>TBG</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fl1\|1fl1]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF010430 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37296 Human herpesvirus 8])</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=2pbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pbk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pbk RCSB], [http://www.ebi.ac.uk/pdbsum/2pbk PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pb/2pbk_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The herpesvirus proteases are an example in which allosteric regulation of an enzyme activity is achieved through the formation of quaternary structure. Here, we report a 1.7 A resolution structure of Kaposi's sarcoma-associated herpesvirus protease in complex with a hexapeptide transition state analogue that stabilizes the dimeric state of the enzyme. Extended substrate binding sites are induced upon peptide binding. In particular, 104 A2 of surface are buried in the newly formed S4 pocket when tyrosine binds at this site. The peptide inhibitor also induces a rearrangement of residues that stabilizes the oxyanion hole and the dimer interface. Concomitant with the structural changes, an increase in catalytic efficiency of the enzyme results upon extended substrate binding. A nearly 20-fold increase in kcat/KM results upon extending the peptide substrate from a tetrapeptide to a hexapeptide exclusively due to a KM effect. This suggests that the mechanism by which herpesvirus proteases achieve their high specificity is by using extended substrates to modulate both the structure and activity of the enzyme.

-	~~{{STRUCTURE_2pbk\| PDB=2pbk \| SCENE= }}~~	+	Substrate modulation of enzyme activity in the herpesvirus protease family.,Lazic A, Goetz DH, Nomura AM, Marnett AB, Craik CS J Mol Biol. 2007 Nov 2;373(4):913-23. Epub 2007 Aug 16. PMID:17870089<ref>PMID:17870089</ref>

-	~~===Crystal structure~~ of ~~KSHV protease in complex with hexapeptide phosphonate inhibitor===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17870089}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2pbk]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Human_herpesvirus_8 Human herpesvirus 8]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2PBK OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017870089<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Human herpesvirus 8]]		[[Category: Human herpesvirus 8]]
	[[Category: Goetz, D H.]]		[[Category: Goetz, D H.]]

OCA: Protected "2pbk" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 11:15:13 GMT

Protected "2pbk" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:15, 7 January 2013

OCA at 11:15, 7 January 2013

OCA — Mon, 07 Jan 2013 11:15:10 GMT

←Older revision		Revision as of 11:15, 7 January 2013
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-	{{Seed}}
	[[Image:2pbk.png\|left\|200px]]		[[Image:2pbk.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2pbk", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2pbk\| PDB=2pbk \| SCENE= }}		{{STRUCTURE_2pbk\| PDB=2pbk \| SCENE= }}

	===Crystal structure of KSHV protease in complex with hexapeptide phosphonate inhibitor===		===Crystal structure of KSHV protease in complex with hexapeptide phosphonate inhibitor===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17870089}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17870089 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17870089}}		{{ABSTRACT_PUBMED_17870089}}

	==About this Structure==		==About this Structure==
-	~~2PBK~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Human_herpesvirus_8 Human herpesvirus 8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PBK OCA].	+	[[2pbk]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_herpesvirus_8 Human herpesvirus 8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PBK OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17870089~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017870089</ref><references group="xtra"/>
	[[Category: Human herpesvirus 8]]		[[Category: Human herpesvirus 8]]
	[[Category: Goetz, D H.]]		[[Category: Goetz, D H.]]
	[[Category: Lazic, A.]]		[[Category: Lazic, A.]]
	[[Category: Herpesvirus protease]]		[[Category: Herpesvirus protease]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]
	[[Category: Kshv]]		[[Category: Kshv]]
	[[Category: Kshv protease]]		[[Category: Kshv protease]]
	[[Category: Viral protease]]		[[Category: Viral protease]]
	[[Category: Viral protein]]		[[Category: Viral protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 21:01:52 2009''

OCA at 19:01, 17 February 2009

OCA — Tue, 17 Feb 2009 19:01:54 GMT

←Older revision		Revision as of 19:01, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2PBK is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Human_herpesvirus_8 Human herpesvirus 8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PBK OCA].	+	2PBK is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Human_herpesvirus_8 Human herpesvirus 8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PBK OCA].

	==Reference==		==Reference==
-	~~Substrate modulation of enzyme activity in the herpesvirus protease family., Lazic A, Goetz DH, Nomura AM, Marnett AB, Craik CS, J Mol Biol. 2007 Nov 2;373(4):913-23. Epub 2007 Aug 16.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17870089 17870089]~~	+	<ref group="xtra">PMID:17870089</ref><references group="xtra"/>
	[[Category: Human herpesvirus 8]]		[[Category: Human herpesvirus 8]]
-	[[Category: Single protein]]
	[[Category: Goetz, D H.]]		[[Category: Goetz, D H.]]
	[[Category: Lazic, A.]]		[[Category: Lazic, A.]]
Line 34:		Line 33:
	[[Category: Viral protein]]		[[Category: Viral protein]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 05~~:03:~~11 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 21:01:52 2009''

OCA at 02:03, 29 July 2008

OCA — Tue, 29 Jul 2008 02:03:11 GMT

←Older revision		Revision as of 02:03, 29 July 2008
Line 1:		Line 1:
-	[[Image:2pbk.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2pbk.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_2pbk\| PDB=2pbk \| SCENE= }}		{{STRUCTURE_2pbk\| PDB=2pbk \| SCENE= }}

-	~~'''~~Crystal structure of KSHV protease in complex with hexapeptide phosphonate inhibitor~~'''~~	+	===Crystal structure of KSHV protease in complex with hexapeptide phosphonate inhibitor===


-	~~==Overview==~~	+	<!--
-	The ~~herpesvirus proteases are an example in which allosteric regulation of an enzyme activity is achieved through the formation of quaternary structure. Here~~, ~~we report a 1.7 A resolution structure of Kaposi's sarcoma-associated herpesvirus protease in complex with a hexapeptide transition state analogue that stabilizes~~ the ~~dimeric state of~~ the ~~enzyme. Extended substrate binding sites are induced upon peptide binding. In particular, 104 A2 of surface are buried in the newly formed S4 pocket when tyrosine binds~~ at ~~this site~~. ~~The peptide inhibitor also induces a rearrangement of residues that stabilizes the oxyanion hole and the dimer interface~~. ~~Concomitant with the structural changes~~, ~~an increase in catalytic efficiency of~~ the ~~enzyme results upon extended substrate binding~~. ~~A nearly 20~~-fold increase in kcat/KM results upon extending the peptide substrate from a tetrapeptide to a hexapeptide exclusively due to a KM effect. This suggests that the mechanism by which herpesvirus proteases achieve their high specificity is by using extended substrates to modulate both the structure and activity of the enzyme.	+	The line below this paragraph, {{ABSTRACT_PUBMED_17870089}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 17870089 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_17870089}}

	==About this Structure==		==About this Structure==
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	[[Category: Viral protease]]		[[Category: Viral protease]]
	[[Category: Viral protein]]		[[Category: Viral protein]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 12~~:47:06 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 05:03:11 2008''