5hn8 - Revision history

OCA at 10:47, 16 August 2023

OCA — Wed, 16 Aug 2023 10:47:47 GMT

←Older revision		Revision as of 10:47, 16 August 2023
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	<StructureSection load='5hn8' size='340' side='right'caption='[[5hn8]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='5hn8' size='340' side='right'caption='[[5hn8]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hn8]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Plavs Plavs~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HN8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5HN8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hn8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Plasmodium_vivax_Sal-1 Plasmodium vivax Sal-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HN8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HN8 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=HXK:2~~-{[~~3-HYDROXY-5-(OCTYLOXY)BENZYL~~]~~SULFANYL}BENZOIC+ACID'>HXK</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.7Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">[~~[5hn7\|5hn7~~]~~], [[5hn9\|5hn9]], [[5hna\|5hna]]</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HXK:2-{[3-HYDROXY-5-(OCTYLOXY)BENZYL]SULFANYL}BENZOIC+ACID'>HXK</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">PVX_092040 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=126793 PLAVS])~~</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=5hn8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hn8 OCA], [https://pdbe.org/5hn8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hn8 RCSB], [https://www.ebi.ac.uk/pdbsum/5hn8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hn8 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=5hn8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hn8 OCA], [~~http~~://pdbe.org/5hn8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5hn8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5hn8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5hn8 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A5K4U6_PLAVS A5K4U6_PLAVS]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Plavs~~]]	+	[[Category: Plasmodium vivax Sal-1]]
-	[[Category: Liu, Y L]]	+	[[Category: Liu Y-L]]
-	[[Category: Oldfield, E]]	+	[[Category: Oldfield E]]
-	[[Category: Zhang, Y]]	+	[[Category: Zhang Y]]
-	~~[[Category: Transferase-transferase inhibitor complex~~]]	+

OCA at 09:06, 4 December 2019

OCA — Wed, 04 Dec 2019 09:06:13 GMT

←Older revision		Revision as of 09:06, 4 December 2019
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	==Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate synthase complexed with BPH-1182==		==Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate synthase complexed with BPH-1182==
-	<StructureSection load='5hn8' size='340' side='right' caption='[[5hn8]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='5hn8' size='340' side='right'caption='[[5hn8]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hn8]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HN8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HN8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hn8]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Plavs Plavs]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HN8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HN8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HXK:2-{[3-HYDROXY-5-(OCTYLOXY)BENZYL]SULFANYL}BENZOIC+ACID'>HXK</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HXK:2-{[3-HYDROXY-5-(OCTYLOXY)BENZYL]SULFANYL}BENZOIC+ACID'>HXK</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hn7\|5hn7]], [[5hn9\|5hn9]], [[5hna\|5hna]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hn7\|5hn7]], [[5hn9\|5hn9]], [[5hna\|5hna]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PVX_092040 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=126793 PLAVS])</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=5hn8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hn8 OCA], [http://pdbe.org/5hn8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hn8 RCSB], [http://www.ebi.ac.uk/pdbsum/5hn8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hn8 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=5hn8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hn8 OCA], [http://pdbe.org/5hn8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hn8 RCSB], [http://www.ebi.ac.uk/pdbsum/5hn8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hn8 ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Plavs]]
	[[Category: Liu, Y L]]		[[Category: Liu, Y L]]
	[[Category: Oldfield, E]]		[[Category: Oldfield, E]]
	[[Category: Zhang, Y]]		[[Category: Zhang, Y]]
	[[Category: Transferase-transferase inhibitor complex]]		[[Category: Transferase-transferase inhibitor complex]]

OCA at 21:07, 10 September 2016

OCA — Sat, 10 Sep 2016 21:07:13 GMT

←Older revision		Revision as of 21:07, 10 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5hn8 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate synthase complexed with BPH-1182==
		+	<StructureSection load='5hn8' size='340' side='right' caption='[[5hn8]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5hn8]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HN8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HN8 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HXK:2-{[3-HYDROXY-5-(OCTYLOXY)BENZYL]SULFANYL}BENZOIC+ACID'>HXK</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hn7\|5hn7]], [[5hn9\|5hn9]], [[5hna\|5hna]]</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=5hn8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hn8 OCA], [http://pdbe.org/5hn8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hn8 RCSB], [http://www.ebi.ac.uk/pdbsum/5hn8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hn8 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We report a molecular dynamics investigation of the structure, function, and inhibition of geranylgeranyl diphosphate synthase (GGPPS), a potential drug target, from the malaria parasite Plasmodium vivax. We discovered several GGPPS inhibitors, benzoic acids, and determined their structures crystallographically. We then used molecular dynamics simulations to investigate the dynamics of three such inhibitors and two bisphosphonate inhibitors, zoledronate and a lipophilic analogue of zoledronate, as well as the enzyme's product, GGPP. We were able to identify the main motions that govern substrate binding and product release as well as the molecular features required for GGPPS inhibition by both classes of inhibitor. The results are of broad general interest because they represent the first detailed investigation of the mechanism of action, and inhibition, of an important antimalarial drug target, geranylgeranyl diphosphate synthase, and may help guide the development of other, novel inhibitors as new drug leads.

-	~~Authors~~: Liu, Y~~.-L., Zhang~~, Y., ~~Oldfield~~, E.	+	Dynamic Structure and Inhibition of a Malaria Drug Target: Geranylgeranyl Diphosphate Synthase.,G Ricci C, Liu YL, Zhang Y, Wang Y, Zhu W, Oldfield E, McCammon JA Biochemistry. 2016 Sep 1. PMID:27564465<ref>PMID:27564465</ref>

-	~~Description: Crystal structure~~ of ~~Plasmodium vivax geranylgeranylpyrophosphate synthase complexed with BPH-1182~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Zhang~~, Y]]	+	<div class="pdbe-citations 5hn8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Liu, Y L]]
	[[Category: Oldfield, E]]		[[Category: Oldfield, E]]
-	[[Category: ~~Liu~~, Y.-L]]	+	[[Category: Zhang, Y]]
		+	[[Category: Transferase-transferase inhibitor complex]]

OCA at 00:56, 21 February 2016

OCA — Sun, 21 Feb 2016 00:56:46 GMT

←Older revision		Revision as of 00:56, 21 February 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5hn8 is ON HOLD	+	The entry 5hn8 is ON HOLD until Paper Publication

	Authors: Liu, Y.-L., Zhang, Y., Oldfield, E.		Authors: Liu, Y.-L., Zhang, Y., Oldfield, E.

OCA: Protected "5hn8" [edit=sysop:move=sysop]

OCA — Thu, 28 Jan 2016 00:55:12 GMT

Protected "5hn8" [edit=sysop:move=sysop]

←Older revision

Revision as of 00:55, 28 January 2016

OCA: New page: '''Unreleased structure''' The entry 5hn8 is ON HOLD Authors: Liu, Y.-L., Zhang, Y., Oldfield, E. Description: Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate synthas...

OCA — Thu, 28 Jan 2016 00:55:11 GMT

New page: '''Unreleased structure''' The entry 5hn8 is ON HOLD Authors: Liu, Y.-L., Zhang, Y., Oldfield, E. Description: Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate synthas...

New page

'''Unreleased structure'''

The entry 5hn8 is ON HOLD

Authors: Liu, Y.-L., Zhang, Y., Oldfield, E.

Description: Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate synthase complexed with BPH-1182
[[Category: Unreleased Structures]]
[[Category: Zhang, Y]]
[[Category: Oldfield, E]]
[[Category: Liu, Y.-L]]