› 3b9f

X-ray diffraction
1.6Å resolution

1.6 A structure of the PCI-thrombin-heparin complex

Released:
DOI: 10.2210/pdb3b9f/pdb
PDB entry 3b9f coloured by chain, front view.
PDB entry 3b9f coloured by chain, side view.
PDB entry 3b9f coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular basis of thrombin recognition by protein C inhibitor revealed by the 1.6-A structure of the heparin-bridged complex.
Li W, Adams TE, Nangalia J, Esmon CT, Huntington JA
Proc Natl Acad Sci U S A 105 4661-6 (2008)
PMID: 18362344

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:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133133 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (5 distinct):
Thrombin light chain Chain: L
Molecule details ›
Chain: L
Length: 49 amino acids
Theoretical weight: 5.64 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P00734 (Residues: 315-363; Coverage: 8%)
Gene name: F2
Sequence domains: Thrombin light chain
Structure domains: Thrombin light chain domain
Thrombin heavy chain Chain: H
Molecule details ›
Chain: H
Length: 259 amino acids
Theoretical weight: 29.76 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
Plasma serine protease inhibitor Chain: I
Molecule details ›
Chain: I
Length: 395 amino acids
Theoretical weight: 44.53 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9N2I2 (Residues: 32-404; Coverage: 96%)
Gene name: SERPINA5
Sequence domains: Serpin (serine protease inhibitor)
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: SGN, IDS
Carbohydrate polymer
2 bound ligands:
Ligand SO4 3 x SO4
Ligand GOL 5 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P1
Unit cell:
a: 44.055Å b: 48.825Å c: 97.85Å
α: 78.72° β: 81.52° γ: 77.69°
R-values:
R R work R free
0.208 0.208 0.234
Expression system: Escherichia coli

Quick links

Citations

10 review citations

Regulation of the protein C anticoagulant and antiinflammatory pathways.
Rezaie AR. (2010)
9 more

7 mentions without citation

Demystifying heparan sulfate-protein interactions.
Xu et al. (2014)
6 more