› 5zkq

X-ray diffraction
2.9Å resolution

Crystal structure of the human platelet-activating factor receptor in complex with ABT-491

Released:
DOI: 10.2210/pdb5zkq/pdb
PDB entry 5zkq coloured by chain, front view.
PDB entry 5zkq coloured by chain, side view.
PDB entry 5zkq 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

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:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132970 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Endolysin; Platelet-activating factor receptor Chains: A, B
Molecule details ›
Chains: A, B
Length: 438 amino acids
Theoretical weight: 50.13 KDa
Source organisms: Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P25105 (Residues: 2-218, 224-316; Coverage: 91%)
  • Canonical: P00720 (Residues: 61-161; Coverage: 62%)
Gene names: E, PAFR, PTAFR
Sequence domains:

Ligands and Environments

4 bound ligands:
Ligand 9EU 2 x 9EU
Ligand OLC 7 x OLC
Ligand ZN 2 x ZN
Ligand SO4 6 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: C2
Unit cell:
a: 86.22Å b: 166.54Å c: 100.31Å
α: 90° β: 100° γ: 90°
R-values:
R R work R free
0.204 0.203 0.235
Expression system: Spodoptera frugiperda

Quick links

Citations

5 review citations

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

14 mentions without citation

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