PDBe 1riw

X-ray diffraction
2.04Å resolution

Thrombin in complex with natural product inhibitor Oscillarin

Released:

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 tetramer (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Thrombin light chain Chain: A
Molecule details ›
Chain: A
Length: 36 amino acids
Theoretical weight: 4.1 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 328-363; Coverage: 6%)
Gene name: F2
Thrombin heavy chain Chain: B
Molecule details ›
Chain: B
Length: 147 amino acids
Theoretical weight: 17.07 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 364-510; Coverage: 25%)
Gene name: F2
Structure domains: Trypsin-like serine proteases
Thrombin heavy chain Chain: C
Molecule details ›
Chain: C
Length: 105 amino acids
Theoretical weight: 11.97 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 518-622; Coverage: 18%)
Gene name: F2
Structure domains: Trypsin-like serine proteases
Hirudin-2B Chain: D
Molecule details ›
Chain: D
Length: 11 amino acids
Theoretical weight: 1.49 KDa
Source organism: Hirudo medicinalis
Expression system: Not provided
UniProt:
  • Canonical: P28506 (Residues: 55-65; Coverage: 17%)

Ligands and Environments

3 bound ligands:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: C2
Unit cell:
a: 71.055Å b: 72.366Å c: 70.83Å
α: 90° β: 100.19° γ: 90°
R-values:
R R work R free
0.213 0.213 0.232
Expression system: Not provided