PDBe 3bef

X-ray diffraction
2.2Å resolution

Crystal structure of thrombin bound to the extracellular fragment of PAR1

Released:
Source organism: Homo sapiens
Primary publication:
Structural identification of the pathway of long-range communication in an allosteric enzyme.
Proc. Natl. Acad. Sci. U.S.A. 105 1832-7 (2008)
PMID: 18250335

Function and Biology Details

Reaction catalysed:
Selective cleavage of Arg-|-Gly bonds in fibrinogen to form fibrin and release fibrinopeptides A and B.
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Thrombin light chain Chains: A, D
Molecule details ›
Chains: A, D
Length: 46 amino acids
Theoretical weight: 5.37 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P00734 (Residues: 320-363; Coverage: 7%)
Gene name: F2
Structure domains: Thrombin light chain domain
Thrombin heavy chain Chains: B, E
Molecule details ›
Chains: B, E
Length: 259 amino acids
Theoretical weight: 29.78 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P00734 (Residues: 364-622; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Proteinase-activated receptor 1 Chains: C, F
Molecule details ›
Chains: C, F
Length: 9 amino acids
Theoretical weight: 1.23 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P25116 (Residues: 49-57; Coverage: 2%)
Gene names: CF2R, F2R, PAR1, TR

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-BM-C
Spacegroup: P1
Unit cell:
a: 46.06Å b: 50.342Å c: 85.078Å
α: 76.89° β: 84.3° γ: 73.69°
R-values:
R R work R free
0.207 0.207 0.248
Expression system: Cricetulus griseus