› 3vw7

X-ray diffraction
2.2Å resolution

Crystal structure of human protease-activated receptor 1 (PAR1) bound with antagonist vorapaxar at 2.2 angstrom

Released:
DOI: 10.2210/pdb3vw7/pdb
PDB entry 3vw7 coloured by chain, front view.3vw7 coloured by chain, front view. This structure contains:
  • 1 copy of Endolysin;
  • 1 copy of 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]fur an-6-yl]carbamate;
  • 9 copies of (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate;
  • 1 copy of CHLORIDE ION;
  • 1 copy of SODIUM ION;
  • 1 copy of water.
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PDB entry 3vw7 coloured by chain, side view.3vw7 coloured by chain, side view. This structure contains:
  • 1 copy of Endolysin;
  • 1 copy of 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]fur an-6-yl]carbamate;
  • 9 copies of (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate;
  • 1 copy of CHLORIDE ION;
  • 1 copy of SODIUM ION;
  • 1 copy of water.
">
PDB entry 3vw7 coloured by chain, top view.3vw7 coloured by chain, top view. This structure contains:
  • 1 copy of Endolysin;
  • 1 copy of 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]fur an-6-yl]carbamate;
  • 9 copies of (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate;
  • 1 copy of CHLORIDE ION;
  • 1 copy of SODIUM ION;
  • 1 copy of water.
">
Source organisms:
Primary publication:
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
OpenAccess logo Nature 492 387-92 (2012)
PMID: 23222541

Function and Biology Details

Reaction catalysed: 
Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132971 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Endolysin; Proteinase-activated receptor 1 Chain: A
Molecule details ›
Chain: A
Length: 484 amino acids
Theoretical weight: 54.34 KDa
Source organisms: Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P25116 (Residues: 86-301, 303-395; Coverage: 77%)
  • Canonical: P00720 (Residues: 2-161; Coverage: 98%)
Gene names: CF2R, E, F2R, PAR1, TR
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand VPX 1 x VPX
Ligand OLC 9 x OLC
Ligand CL 1 x CL
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P212121
Unit cell:
a: 44.044Å b: 71.46Å c: 172.187Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.219 0.218 0.235
Expression system: Spodoptera frugiperda

Quick links

Citations

69 review citations

Molecular signatures of G-protein-coupled receptors.
Venkatakrishnan et al. (2013)
68 more

84 mentions without citation

Microbial and animal rhodopsins: structures, functions, and molecular mechanisms.
Ernst et al. (2014)
83 more