5zkq - Revision history

OCA at 08:59, 22 November 2023

OCA — Wed, 22 Nov 2023 08:59:10 GMT

←Older revision		Revision as of 08:59, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5zkq' size='340' side='right'caption='[[5zkq]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='5zkq' size='340' side='right'caption='[[5zkq]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zkq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZKQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5ZKQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zkq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZKQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9EU:4-ethynyl-3-{3-fluoro-4-[(2-methyl-1H-imidazo[4,5-c]pyridin-1-yl)methyl]benzene-1-carbonyl}-N,N-dimethyl-1H-indole-1-carboxamide'>9EU</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.9Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9EU:4-ethynyl-3-{3-fluoro-4-[(2-methyl-1H-imidazo[4,5-c]pyridin-1-yl)methyl]benzene-1-carbonyl}-N,N-dimethyl-1H-indole-1-carboxamide'>9EU</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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~~://proteopedia.org/fgij/fg.htm?mol=5zkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zkq OCA], [~~http~~://pdbe.org/5zkq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zkq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zkq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zkq 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=5zkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zkq OCA], [https://pdbe.org/5zkq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zkq RCSB], [https://www.ebi.ac.uk/pdbsum/5zkq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zkq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PTAFR_HUMAN PTAFR_HUMAN]] Receptor for platelet activating factor, a chemotactic phospholipid mediator that possesses potent inflammatory, smooth-muscle contractile and hypotensive activity. Seems to mediate its action via a G protein that activates a phosphatidylinositol-calcium second messenger system.<ref>PMID:1281995</ref> <ref>PMID:1374385</ref> <ref>PMID:1656963</ref> <ref>PMID:1657923</ref>	+	[https://www.uniprot.org/uniprot/PTAFR_HUMAN PTAFR_HUMAN] Receptor for platelet activating factor, a chemotactic phospholipid mediator that possesses potent inflammatory, smooth-muscle contractile and hypotensive activity. Seems to mediate its action via a G protein that activates a phosphatidylinositol-calcium second messenger system.<ref>PMID:1281995</ref> <ref>PMID:1374385</ref> <ref>PMID:1656963</ref> <ref>PMID:1657923</ref> [https://www.uniprot.org/uniprot/ENLYS_BPT4 ENLYS_BPT4] Endolysin with lysozyme activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.<ref>PMID:22389108</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia virus T4]]
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Lysozyme]]~~	+	[[Category: Cao C]]
-	[[Category: Cao, C]]	+	[[Category: Wu B]]
-	[[Category: Wu, B]]	+	[[Category: Zhang XC]]
-	[[Category: Zhang~~, X C~~]]	+	[[Category: Zhao Q]]
-	[[Category: Zhao, Q]]	+
-	~~[[Category: Complex]]~~	+
-	~~[[Category: G protein-coupled receptor]]~~	+
-	~~[[Category: Platelet-activating factor receptor]]~~	+
-	~~[[Category: Signaling protein~~]]	+

OCA at 21:21, 28 October 2020

OCA — Wed, 28 Oct 2020 21:21:00 GMT

←Older revision		Revision as of 21:21, 28 October 2020
Line 1:		Line 1:

	==Crystal structure of the human platelet-activating factor receptor in complex with ABT-491==		==Crystal structure of the human platelet-activating factor receptor in complex with ABT-491==
-	<StructureSection load='5zkq' size='340' side='right' caption='[[5zkq]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='5zkq' size='340' side='right'caption='[[5zkq]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zkq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZKQ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZKQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zkq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZKQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ZKQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9EU:4-ethynyl-3-{3-fluoro-4-[(2-methyl-1H-imidazo[4,5-c]pyridin-1-yl)methyl]benzene-1-carbonyl}-N,N-dimethyl-1H-indole-1-carboxamide'>9EU</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=9EU:4-ethynyl-3-{3-fluoro-4-[(2-methyl-1H-imidazo[4,5-c]pyridin-1-yl)methyl]benzene-1-carbonyl}-N,N-dimethyl-1H-indole-1-carboxamide'>9EU</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=5zkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zkq OCA], [http://pdbe.org/5zkq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zkq RCSB], [http://www.ebi.ac.uk/pdbsum/5zkq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zkq ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5zkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zkq OCA], [http://pdbe.org/5zkq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zkq RCSB], [http://www.ebi.ac.uk/pdbsum/5zkq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zkq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Cao, C]]		[[Category: Cao, C]]

OCA at 05:45, 20 June 2018

OCA — Wed, 20 Jun 2018 05:45:25 GMT

←Older revision		Revision as of 05:45, 20 June 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zkq is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of the human platelet-activating factor receptor in complex with ABT-491==
		+	<StructureSection load='5zkq' size='340' side='right' caption='[[5zkq]], [[Resolution\|resolution]] 2.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5zkq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZKQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9EU:4-ethynyl-3-{3-fluoro-4-[(2-methyl-1H-imidazo[4,5-c]pyridin-1-yl)methyl]benzene-1-carbonyl}-N,N-dimethyl-1H-indole-1-carboxamide'>9EU</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=5zkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zkq OCA], [http://pdbe.org/5zkq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zkq RCSB], [http://www.ebi.ac.uk/pdbsum/5zkq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zkq ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PTAFR_HUMAN PTAFR_HUMAN]] Receptor for platelet activating factor, a chemotactic phospholipid mediator that possesses potent inflammatory, smooth-muscle contractile and hypotensive activity. Seems to mediate its action via a G protein that activates a phosphatidylinositol-calcium second messenger system.<ref>PMID:1281995</ref> <ref>PMID:1374385</ref> <ref>PMID:1656963</ref> <ref>PMID:1657923</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Platelet-activating-factor receptor (PAFR) responds to platelet-activating factor (PAF), a phospholipid mediator of cell-to-cell communication that exhibits diverse physiological effects. PAFR is considered an important drug target for treating asthma, inflammation and cardiovascular diseases. Here we report crystal structures of human PAFR in complex with the antagonist SR 27417 and the inverse agonist ABT-491 at 2.8-A and 2.9-A resolution, respectively. The structures, supported by molecular docking of PAF, provide insights into the signal-recognition mechanisms of PAFR. The PAFR-SR 27417 structure reveals an unusual conformation showing that the intracellular tips of helices II and IV shift outward by 13 A and 4 A, respectively, and helix VIII adopts an inward conformation. The PAFR structures, combined with single-molecule FRET and cell-based functional assays, suggest that the conformational change in the helical bundle is ligand dependent and plays a critical role in PAFR activation, thus greatly extending knowledge about signaling by G-protein-coupled receptors.

-	~~Authors~~:	+	Structural basis for signal recognition and transduction by platelet-activating-factor receptor.,Cao C, Tan Q, Xu C, He L, Yang L, Zhou Y, Zhou Y, Qiao A, Lu M, Yi C, Han GW, Wang X, Li X, Yang H, Rao Z, Jiang H, Zhao Y, Liu J, Stevens RC, Zhao Q, Zhang XC, Wu B Nat Struct Mol Biol. 2018 Jun;25(6):488-495. doi: 10.1038/s41594-018-0068-y. Epub, 2018 May 28. PMID:29808000<ref>PMID:29808000</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5zkq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Lysozyme]]
		+	[[Category: Cao, C]]
		+	[[Category: Wu, B]]
		+	[[Category: Zhang, X C]]
		+	[[Category: Zhao, Q]]
		+	[[Category: Complex]]
		+	[[Category: G protein-coupled receptor]]
		+	[[Category: Platelet-activating factor receptor]]
		+	[[Category: Signaling protein]]

OCA at 06:32, 2 May 2018

OCA — Wed, 02 May 2018 06:32:03 GMT

←Older revision		Revision as of 06:32, 2 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 04 Apr 2018 04:32:05 GMT

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

←Older revision

Revision as of 04:32, 4 April 2018

OCA: New page: '''Unreleased structure''' The entry 5zkq is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 04 Apr 2018 04:32:03 GMT

New page: '''Unreleased structure''' The entry 5zkq is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5zkq is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]