PDBe 1nm6

X-ray diffraction
1.8Å resolution

thrombin in complex with selective macrocyclic inhibitor at 1.8A

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 dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Thrombin heavy chain Chain: A
Molecule details ›
Chain: A
Length: 287 amino acids
Theoretical weight: 33.08 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 335-621; Coverage: 48%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Hirudin-2 Chain: B
Molecule details ›
Chain: B
Length: 11 amino acids
Theoretical weight: 1.43 KDa
Source organism: Hirudo medicinalis
Expression system: Not provided
UniProt:
  • Canonical: P28504 (Residues: 55-64; Coverage: 15%)

Ligands and Environments

1 bound ligand:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: C2
Unit cell:
a: 69.7Å b: 71.4Å c: 72.3Å
α: 90° β: 100.5° γ: 90°
R-values:
R R work R free
0.216 0.216 0.238
Expression system: Not provided