PDBe 4ax9

X-ray diffraction
1.9Å resolution

Human thrombin complexed with Napsagatran, RO0466240

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 heavy chain Chain: H
Molecule details ›
Chain: H
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: I
Molecule details ›
Chain: I
Length: 11 amino acids
Theoretical weight: 1.41 KDa
Source organism: Hirudo medicinalis
UniProt:
  • Canonical: P01050 (Residues: 55-65; Coverage: 17%)
Thrombin light chain Chain: L
Molecule details ›
Chain: L
Length: 28 amino acids
Theoretical weight: 3.3 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 334-361; Coverage: 5%)
Gene name: F2

Ligands and Environments

3 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
Spacegroup: C2
Unit cell:
a: 71.4Å b: 72.04Å c: 72.7Å
α: 90° β: 100.8° γ: 90°
R-values:
R R work R free
0.163 0.161 0.196