PDBe 3p6z

X-ray diffraction
1.7Å resolution

Structural basis of thrombin mediated factor V activation: essential role of the hirudin-like sequence Glu666-Glu672 for processing at the heavy chain-B domain junction

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 Chains: A, G
Molecule details ›
Chains: A, G
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 Chains: B, H
Molecule details ›
Chains: B, 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
Coagulation factor V heavy chain Chains: C, I
Molecule details ›
Chains: C, I
Length: 71 amino acids
Theoretical weight: 8.39 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P12259 (Residues: 685-737; Coverage: 2%)
Gene name: F5

Ligands and Environments


No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P1
Unit cell:
a: 52.208Å b: 62.259Å c: 67.51Å
α: 99.38° β: 110.46° γ: 92.26°
R-values:
R R work R free
0.201 0.2 0.239
Expression system: Escherichia coli BL21(DE3)