PDBe 1e0f

X-ray diffraction
3.1Å resolution

Crystal structure of the human alpha-thrombin-haemadin complex: an exosite II-binding inhibitor


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
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero nonamer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Thrombin light chain Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 36 amino acids
Theoretical weight: 4.1 KDa
Source organism: Homo sapiens
  • Canonical: P00734 (Residues: 328-363; Coverage: 6%)
Gene name: F2
Thrombin heavy chain Chains: D, E, F
Molecule details ›
Chains: D, E, F
Length: 259 amino acids
Theoretical weight: 29.79 KDa
Source organism: Homo sapiens
  • Canonical: P00734 (Residues: 364-622; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Thrombininhibitor Chains: I, J, K
Molecule details ›
Chains: I, J, K
Length: 57 amino acids
Theoretical weight: 6.26 KDa
Source organism: Haemadipsa sylvestris
Expression system: Escherichia coli DH5[alpha]
  • Canonical: Q25163 (Residues: 21-77; Coverage: 100%)
Sequence domains: Haemadin
Structure domains: Thrombin Inhibitor (Hirudin), subunit I

Ligands and Environments

No bound ligands

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RUH2R
Spacegroup: P2
Unit cell:
a: 121.67Å b: 50.57Å c: 129.74Å
α: 90° β: 114.76° γ: 90°
R R work R free
0.208 0.208 0.255
Expression system: Escherichia coli DH5[alpha]