3vw7: Difference between revisions
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<StructureSection load='3vw7' size='340' side='right'caption='[[3vw7]], [[Resolution|resolution]] 2.20Å' scene=''> | <StructureSection load='3vw7' size='340' side='right'caption='[[3vw7]], [[Resolution|resolution]] 2.20Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3vw7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[3vw7]] is a 1 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=3VW7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VW7 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=VPX:ETHYL+[(1R,3AR,4AR,6R,8AR,9S,9AS)-9-{(E)-2-[5-(3-FLUOROPHENYL)PYRIDIN-2-YL]ETHENYL}-1-METHYL-3-OXODODECAHYDRONAPHTHO[2,3-C]FURAN-6-YL]CARBAMATE'>VPX</scene | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=VPX:ETHYL+[(1R,3AR,4AR,6R,8AR,9S,9AS)-9-{(E)-2-[5-(3-FLUOROPHENYL)PYRIDIN-2-YL]ETHENYL}-1-METHYL-3-OXODODECAHYDRONAPHTHO[2,3-C]FURAN-6-YL]CARBAMATE'>VPX</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=3vw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vw7 OCA], [https://pdbe.org/3vw7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vw7 RCSB], [https://www.ebi.ac.uk/pdbsum/3vw7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vw7 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=3vw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vw7 OCA], [https://pdbe.org/3vw7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vw7 RCSB], [https://www.ebi.ac.uk/pdbsum/3vw7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vw7 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[[https://www.uniprot.org/uniprot/PAR1_HUMAN PAR1_HUMAN | [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> [https://www.uniprot.org/uniprot/PAR1_HUMAN PAR1_HUMAN] High affinity receptor for activated thrombin coupled to G proteins that stimulate phosphoinositide hydrolysis. May play a role in platelets activation and in vascular development.<ref>PMID:10079109</ref> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Escherichia virus T4]] | ||
[[Category: Homo sapiens]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Arlow DH]] | |||
[[Category: Arlow | [[Category: Coughlin SR]] | ||
[[Category: Coughlin | [[Category: Dror RO]] | ||
[[Category: Dror | [[Category: Fung JJ]] | ||
[[Category: Fung | [[Category: Green HF]] | ||
[[Category: Green | [[Category: Kobilka BK]] | ||
[[Category: Kobilka | [[Category: Palmer D]] | ||
[[Category: Palmer | [[Category: Pandey A]] | ||
[[Category: Pandey | [[Category: Shaw DE]] | ||
[[Category: Shaw | [[Category: Srinivasan Y]] | ||
[[Category: Srinivasan | [[Category: Weis WI]] | ||
[[Category: Weis | [[Category: Zhang C]] | ||
[[Category: Zhang | [[Category: Zheng Y]] | ||
[[Category: Zheng | |||
Latest revision as of 15:40, 8 November 2023
Crystal structure of human protease-activated receptor 1 (PAR1) bound with antagonist vorapaxar at 2.2 angstromCrystal structure of human protease-activated receptor 1 (PAR1) bound with antagonist vorapaxar at 2.2 angstrom
Structural highlights
FunctionENLYS_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.[1] PAR1_HUMAN High affinity receptor for activated thrombin coupled to G proteins that stimulate phosphoinositide hydrolysis. May play a role in platelets activation and in vascular development.[2] Publication Abstract from PubMedProtease-activated receptor 1 (PAR1) is the prototypical member of a family of G-protein-coupled receptors that mediate cellular responses to thrombin and related proteases. Thrombin irreversibly activates PAR1 by cleaving the amino-terminal exodomain of the receptor, which exposes a tethered peptide ligand that binds the heptahelical bundle of the receptor to affect G-protein activation. Here we report the 2.2 A resolution crystal structure of human PAR1 bound to vorapaxar, a PAR1 antagonist. The structure reveals an unusual mode of drug binding that explains how a small molecule binds virtually irreversibly to inhibit receptor activation by the tethered ligand of PAR1. In contrast to deep, solvent-exposed binding pockets observed in other peptide-activated G-protein-coupled receptors, the vorapaxar-binding pocket is superficial but has little surface exposed to the aqueous solvent. Protease-activated receptors are important targets for drug development. The structure reported here will aid the development of improved PAR1 antagonists and the discovery of antagonists to other members of this receptor family. High-resolution crystal structure of human protease-activated receptor 1.,Zhang C, Srinivasan Y, Arlow DH, Fung JJ, Palmer D, Zheng Y, Green HF, Pandey A, Dror RO, Shaw DE, Weis WI, Coughlin SR, Kobilka BK Nature. 2012 Dec 20;492(7429):387-92. doi: 10.1038/nature11701. Epub 2012 Dec 9. PMID:23222541[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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