PDBe 5af9

X-ray diffraction
1.18Å resolution

Thrombin in complex with 4-Methoxy-N-(2-pyridinyl)benzamide

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: 258 amino acids
Theoretical weight: 29.65 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 364-621; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Hirudin variant-2 Chain: I
Molecule details ›
Chain: I
Length: 12 amino acids
Theoretical weight: 1.55 KDa
Source organism: Hirudo medicinalis
Expression system: Not provided
UniProt:
  • Canonical: P09945 (Residues: 61-72; Coverage: 19%)
Thrombin light chain Chain: L
Molecule details ›
Chain: L
Length: 29 amino acids
Theoretical weight: 3.43 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 333-361; Coverage: 5%)
Gene name: F2

Ligands and Environments

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)
Spacegroup: C2
Unit cell:
a: 70.034Å b: 71.246Å c: 72.138Å
α: 90° β: 100.38° γ: 90°
R-values:
R R work R free
0.121 0.121 0.137
Expression system: Not provided