PDBe 2afq

X-ray diffraction
1.93Å resolution

1.9 angstrom crystal structure of wild-type human thrombin in the sodium free state

Released:
Source organism: Homo sapiens
Primary publication:
Crystal structure of wild-type human thrombin in the Na+-free state.
Biochem. J. 392 21-8 (2005)
PMID: 16201969

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:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Thrombin light chain Chains: A, C
Molecule details ›
Chains: A, C
Length: 29 amino acids
Theoretical weight: 3.37 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P00734 (Residues: 332-360; Coverage: 5%)
Gene name: F2
Thrombin heavy chain Chains: B, D
Molecule details ›
Chains: B, D
Length: 259 amino acids
Theoretical weight: 29.78 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P00734 (Residues: 364-622; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SRS BEAMLINE PX9.6
Spacegroup: P21212
Unit cell:
a: 153.34Å b: 82.31Å c: 50.93Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.203 0.197 0.229
Expression system: Escherichia coli