PDBe 2gde

X-ray diffraction
2Å resolution

Thrombin in complex with inhibitor

Released:
Source organisms:
Primary publication:
Total synthesis and structural confirmation of chlorodysinosin A.
J. Am. Chem. Soc. 128 10491-5 (2006)
PMID: 16895415

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 light chain Chain: L
Molecule details ›
Chain: L
Length: 36 amino acids
Theoretical weight: 4.1 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 328-363; Coverage: 6%)
Gene name: F2
Thrombin heavy chain Chain: H
Molecule details ›
Chain: H
Length: 259 amino acids
Theoretical weight: 29.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 364-622; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Hirudin-2 Chain: D
Molecule details ›
Chain: D
Length: 10 amino acids
Theoretical weight: 1.29 KDa
Source organism: Hirudo medicinalis
Expression system: Not provided
UniProt:
  • Canonical: P28504 (Residues: 55-64; Coverage: 15%)

Ligands and Environments

2 bound ligands:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: OTHER
Spacegroup: C2
Unit cell:
a: 70.084Å b: 72.169Å c: 70.357Å
α: 90° β: 99.06° γ: 90°
R-values:
R R work R free
0.211 0.209 0.248
Expression system: Not provided