› 5zkp

X-ray diffraction
2.81Å resolution

Crystal structure of the human platelet-activating factor receptor in complex with SR 27417

Released:
DOI: 10.2210/pdb5zkp/pdb
PDB entry 5zkp coloured by chain, front view.
PDB entry 5zkp coloured by chain, side view.
PDB entry 5zkp coloured by chain, top view.
Source organisms:
Primary publication:
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 25 488-495 (2018)
PMID: 29808000

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132393 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Flavodoxin; Platelet-activating factor receptor Chain: A
Molecule details ›
Chain: A
Length: 466 amino acids
Theoretical weight: 52.43 KDa
Source organisms: Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P25105 (Residues: 2-217, 224-316; Coverage: 90%)
  • Canonical: P00323 (Residues: 3-148; Coverage: 99%)
Gene names: DVU_2680, PAFR, PTAFR
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand 9ER 1 x 9ER
Ligand FMN 1 x FMN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P3221
Unit cell:
a: 67.05Å b: 67.05Å c: 280.25Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.224 0.222 0.259
Expression system: Spodoptera frugiperda

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Citations

5 review citations

Harnessing Ion-Binding Sites for GPCR Pharmacology.
Zarzycka et al. (2019)
4 more

10 mentions without citation

G protein-coupled receptors: structure- and function-based drug discovery.
Yang et al. (2021)
9 more