PDBe 3u8r

X-ray diffraction
1.47Å resolution

Human thrombin complexed with D-Phe-Pro-D-Arg-Ile

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 light chain Chain: L
Molecule details ›
Chain: L
Length: 30 amino acids
Theoretical weight: 3.52 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 334-363; Coverage: 5%)
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
D-Phe-Pro-D-Arg-Ile DERIVED DIRECT THROMBIN INHIBITOR Chain: I
Molecule details ›
Chain: I
Length: 5 amino acids
Theoretical weight: 531 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P212121
Unit cell:
a: 51.563Å b: 76.527Å c: 83.26Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.131 0.129 0.161
Expression system: Not provided