5v5d - Revision history

OCA at 13:41, 4 October 2023

OCA — Wed, 04 Oct 2023 13:41:50 GMT

←Older revision		Revision as of 13:41, 4 October 2023
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	<StructureSection load='5v5d' size='340' side='right'caption='[[5v5d]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5v5d' size='340' side='right'caption='[[5v5d]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v5d]] is a 2 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=5V5D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5V5D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v5d]] is a 2 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=5V5D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5V5D FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=8OY:4~~-{[~~6-(CYCLOHEXYLMETHYL)PYRIDINE-~~2~~-CARBONYL]AMINO}-3-(PHENYLAMINO)BENZOIC+ACID'>8OY</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]] 2.104Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~ORF17 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=37296 HHV~~-8])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8OY:4-{[6-(CYCLOHEXYLMETHYL)PYRIDINE-2-CARBONYL]AMINO}-3-(PHENYLAMINO)BENZOIC+ACID'>8OY</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=5v5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v5d OCA], [~~http~~://pdbe.org/5v5d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5v5d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5v5d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5v5d 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=5v5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v5d OCA], [https://pdbe.org/5v5d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5v5d RCSB], [https://www.ebi.ac.uk/pdbsum/5v5d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5v5d ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O40922_HHV8 O40922_HHV8]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5v5d" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5v5d" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Virus protease 3D structures\|Virus protease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Hhv-~~8]]	+	[[Category: Human gammaherpesvirus 8]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Acker~~, T M~~]]	+	[[Category: Acker TM]]
-	[[Category: Craik~~, C S~~]]	+	[[Category: Craik CS]]
-	[[Category: Fraser~~, J S~~]]	+	[[Category: Fraser JS]]
-	[[Category: Thompson~~, M C]]~~	+	[[Category: Thompson MC]]
-	~~[[Category: Allosteric inhibitor]]~~	+
-	~~[[Category: Herpesvirus]]~~	+
-	~~[[Category: Protease]]~~	+
-	~~[[Category: Viral protein - inhibitor complex~~]]	+

OCA at 09:34, 4 December 2019

OCA — Wed, 04 Dec 2019 09:34:28 GMT

←Older revision		Revision as of 09:34, 4 December 2019
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	==Room temperature (280K) crystal structure of Kaposi's sarcoma-associated herpesvirus protease in complex with allosteric inhibitor (compound 250)==		==Room temperature (280K) crystal structure of Kaposi's sarcoma-associated herpesvirus protease in complex with allosteric inhibitor (compound 250)==
-	<StructureSection load='5v5d' size='340' side='right' caption='[[5v5d]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5v5d' size='340' side='right'caption='[[5v5d]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5v5d]] is a 2 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=5V5D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V5D FirstGlance]. <br>		<table><tr><td colspan='2'>[[5v5d]] is a 2 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=5V5D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V5D FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Hhv-8]]		[[Category: Hhv-8]]
		+	[[Category: Large Structures]]
	[[Category: Acker, T M]]		[[Category: Acker, T M]]
	[[Category: Craik, C S]]		[[Category: Craik, C S]]

OCA at 19:52, 15 November 2017

OCA — Wed, 15 Nov 2017 19:52:56 GMT

←Older revision		Revision as of 19:52, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='5v5d' size='340' side='right' caption='[[5v5d]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5v5d' size='340' side='right' caption='[[5v5d]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v5d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V5D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V5D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v5d]] is a 2 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=5V5D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V5D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OY:4-{[6-(CYCLOHEXYLMETHYL)PYRIDINE-2-CARBONYL]AMINO}-3-(PHENYLAMINO)BENZOIC+ACID'>8OY</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OY:4-{[6-(CYCLOHEXYLMETHYL)PYRIDINE-2-CARBONYL]AMINO}-3-(PHENYLAMINO)BENZOIC+ACID'>8OY</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ORF17 ([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=5v5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v5d OCA], [http://pdbe.org/5v5d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v5d RCSB], [http://www.ebi.ac.uk/pdbsum/5v5d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v5d 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=5v5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v5d OCA], [http://pdbe.org/5v5d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v5d RCSB], [http://www.ebi.ac.uk/pdbsum/5v5d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v5d ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Hhv-8]]
	[[Category: Acker, T M]]		[[Category: Acker, T M]]
	[[Category: Craik, C S]]		[[Category: Craik, C S]]

OCA at 06:03, 17 August 2017

OCA — Thu, 17 Aug 2017 06:03:52 GMT

←Older revision		Revision as of 06:03, 17 August 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=5v5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v5d OCA], [http://pdbe.org/5v5d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v5d RCSB], [http://www.ebi.ac.uk/pdbsum/5v5d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v5d 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=5v5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v5d OCA], [http://pdbe.org/5v5d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v5d RCSB], [http://www.ebi.ac.uk/pdbsum/5v5d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v5d ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Targeting of cryptic binding sites represents an attractive but underexplored approach to modulating protein function with small molecules. Using the dimeric protease (Pr) from Kaposi's sarcoma-associated herpesvirus (KSHV) as a model system, we sought to dissect a putative allosteric network linking a cryptic site at the dimerization interface to enzyme function. Five cryogenic x-ray structures were solved of the monomeric protease with allosteric inhibitors bound to the dimer interface site. Distinct coordinated movements captured by the allosteric inhibitors were also revealed as alternative states in room temperature X-ray data and comparative analyses of other dimeric herpesvirus proteases. A two-step mechanism was elucidated through detailed kinetic analyses and suggests an enzyme isomerization model of inhibition. Finally, a representative allosteric inhibitor from this class was shown to be efficacious in a cellular model of viral infectivity. These studies reveal a coordinated dynamic network of atomic communication linking cryptic binding site occupancy and allosteric inactivation of KHSV Pr that can be exploited to target other members of this clinically relevant family of enzymes.
		+
		+	Allosteric Inhibitors, Crystallography and Comparative Analysis Reveal Network of Coordinated Movement Across Human Herpesvirus Proteases.,Acker TM, Gable JE, Bohn MF, Jaishankar P, Thompson MC, Fraser JS, Renslo AR, Craik CS J Am Chem Soc. 2017 Jul 31. doi: 10.1021/jacs.7b04030. PMID:28759216<ref>PMID:28759216</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5v5d" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:49, 12 April 2017

OCA — Wed, 12 Apr 2017 11:49:17 GMT

←Older revision		Revision as of 11:49, 12 April 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5v5d is ON HOLD~~	+	==Room temperature (280K) crystal structure of Kaposi's sarcoma-associated herpesvirus protease in complex with allosteric inhibitor (compound 250)==
-		+	<StructureSection load='5v5d' size='340' side='right' caption='[[5v5d]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~Authors: Thompson, M.C., Acker, T.M., Fraser, J.S., Craik, C.S.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5v5d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V5D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V5D FirstGlance]. <br>
-	~~Description:~~ Room temperature (280K) crystal structure of Kaposi's sarcoma-associated herpesvirus protease in complex with allosteric inhibitor (compound 250)	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OY:4-{[6-(CYCLOHEXYLMETHYL)PYRIDINE-2-CARBONYL]AMINO}-3-(PHENYLAMINO)BENZOIC+ACID'>8OY</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=5v5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v5d OCA], [http://pdbe.org/5v5d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v5d RCSB], [http://www.ebi.ac.uk/pdbsum/5v5d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v5d ProSAT]</span></td></tr>
-	[[Category: Acker, T.M]]	+	</table>
-	[[Category: ~~Thompson~~, M.C]]	+	__TOC__
-	[[Category: Fraser, J.S]]	+	</StructureSection>
-	[[Category: ~~Craik~~, C.S]]	+	[[Category: Acker, T M]]
		+	[[Category: Craik, C S]]
		+	[[Category: Fraser, J S]]
		+	[[Category: Thompson, M C]]
		+	[[Category: Allosteric inhibitor]]
		+	[[Category: Herpesvirus]]
		+	[[Category: Protease]]
		+	[[Category: Viral protein - inhibitor complex]]

OCA: Protected "5v5d" [edit=sysop:move=sysop]

OCA — Wed, 05 Apr 2017 11:37:22 GMT

Protected "5v5d" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:37, 5 April 2017

OCA: New page: '''Unreleased structure''' The entry 5v5d is ON HOLD Authors: Thompson, M.C., Acker, T.M., Fraser, J.S., Craik, C.S. Description: Room temperature (280K) crystal structure of Kaposi's ...

OCA — Wed, 05 Apr 2017 11:37:21 GMT

New page: '''Unreleased structure''' The entry 5v5d is ON HOLD Authors: Thompson, M.C., Acker, T.M., Fraser, J.S., Craik, C.S. Description: Room temperature (280K) crystal structure of Kaposi's ...

New page

'''Unreleased structure'''

The entry 5v5d is ON HOLD

Authors: Thompson, M.C., Acker, T.M., Fraser, J.S., Craik, C.S.

Description: Room temperature (280K) crystal structure of Kaposi's sarcoma-associated herpesvirus protease in complex with allosteric inhibitor (compound 250)
[[Category: Unreleased Structures]]
[[Category: Acker, T.M]]
[[Category: Thompson, M.C]]
[[Category: Fraser, J.S]]
[[Category: Craik, C.S]]