PDBe 1d3d

X-ray diffraction
2.04Å resolution

CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH BENZOTHIOPHENE INHIBITOR 4

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 trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Thrombin light chain Chain: A
Molecule details ›
Chain: A
Length: 28 amino acids
Theoretical weight: 3.32 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 333-360; Coverage: 5%)
Gene name: F2
Thrombin heavy chain Chain: B
Molecule details ›
Chain: B
Length: 257 amino acids
Theoretical weight: 29.59 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 364-620; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Hirudin variant-1 Chain: H
Molecule details ›
Chain: H
Length: 12 amino acids
Theoretical weight: 1.55 KDa
Source organism: Hirudo medicinalis
UniProt:
  • Canonical: P01050 (Residues: 54-65; Coverage: 19%)

Ligands and Environments

3 bound ligands:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: C2
Unit cell:
a: 71.11Å b: 71.888Å c: 73.321Å
α: 90° β: 100.6° γ: 90°
R-values:
R R work R free
0.175 0.175 0.223