PDBe 2bdy

X-ray diffraction
1.61Å resolution

thrombin in complex with inhibitor

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:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Thrombin heavy chain Chain: A
Molecule details ›
Chain: A
Length: 289 amino acids
Theoretical weight: 33.28 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 334-622; Coverage: 48%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Hirudin-3B' Chain: B
Molecule details ›
Chain: B
Length: 10 amino acids
Theoretical weight: 1.36 KDa
Source organism: Hirudo medicinalis
Expression system: Not provided
UniProt:
  • Canonical: P28511 (Residues: 55-64; Coverage: 15%)

Ligands and Environments

2 bound ligands:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: C2
Unit cell:
a: 69.918Å b: 71.649Å c: 71.234Å
α: 90° β: 99.56° γ: 90°
R-values:
R R work R free
0.194 0.193 0.225
Expression system: Not provided