PDBe 1h8d

X-ray diffraction
1.4Å resolution

X-ray structure of the human alpha-thrombin complex with a tripeptide phosphonate 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:
  • 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: 260 amino acids
Theoretical weight: 29.8 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 364-621; Coverage: 42%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Hirudin variant-1 Chain: I
Molecule details ›
Chain: I
Length: 10 amino acids
Theoretical weight: 1.36 KDa
Source organism: Hirudo medicinalis
UniProt:
  • Canonical: P01050 (Residues: 55-64; Coverage: 15%)
Thrombin light chain Chain: L
Molecule details ›
Chain: L
Length: 29 amino acids
Theoretical weight: 3.4 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 333-360; Coverage: 5%)
Gene name: F2

Ligands and Environments

1 bound ligand:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: SRS BEAMLINE PX7.2
Spacegroup: C2
Unit cell:
a: 70.64Å b: 71.6Å c: 71.9Å
α: 90° β: 100.35° γ: 90°
R-values:
R R work R free
0.17 0.17 0.22