› 2c4f

X-ray diffraction
1.72Å resolution

crystal structure of factor VII.stf complexed with pd0297121

Released:
DOI: 10.2210/pdb2c4f/pdb
PDB entry 2c4f coloured by chain, front view.
PDB entry 2c4f coloured by chain, side view.
PDB entry 2c4f coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The discovery of fluoropyridine-based inhibitors of the factor VIIa/TF complex--Part 2.
Kohrt JT, Filipski KJ, Cody WL, Cai C, Dudley DA, Van Huis CA, Willardsen JA, Narasimhan LS, Zhang E, Rapundalo ST, Saiya-Cork K, Leadley RJ, Edmunds JJ
Bioorg Med Chem Lett 16 1060-4 (2006)
PMID: 16289811

Function and Biology Details

Reaction catalysed: 
Selective cleavage of Arg-|-Ile bond in factor X to form factor Xa.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140353 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Factor VII heavy chain Chain: H
Molecule details ›
Chain: H
Length: 254 amino acids
Theoretical weight: 28.1 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P08709 (Residues: 213-466; Coverage: 57%)
Gene name: F7
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Factor VII light chain Chain: L
Molecule details ›
Chain: L
Length: 142 amino acids
Theoretical weight: 16.36 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P08709 (Residues: 61-202; Coverage: 32%)
Gene name: F7
Sequence domains:
Tissue factor Chain: T
Molecule details ›
Chain: T
Length: 75 amino acids
Theoretical weight: 8.72 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P13726 (Residues: 38-112; Coverage: 29%)
Gene name: F3
Sequence domains: Tissue factor
Structure domains: Immunoglobulins
Tissue factor Chain: U
Molecule details ›
Chain: U
Length: 116 amino acids
Theoretical weight: 13.35 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P13726 (Residues: 123-242; Coverage: 44%)
Gene name: F3
Sequence domains: Interferon-alpha/beta receptor, fibronectin type III
Structure domains: Immunoglobulins

Ligands and Environments

5 bound ligands:
Ligand CA 5 x CA
Ligand GIL 1 x GIL
Ligand GLC 1 x GLC
Ligand FUC 1 x FUC
Ligand NAG 1 x NAG
1 modified residue:
Ligand CGU 10 x CGU

Experiments and Validation Details

Entry percentile scores
X-ray source: APS
Spacegroup: P212121
Unit cell:
a: 70.993Å b: 81.302Å c: 125.86Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.228 0.228 not available
Expression system: Not provided

Quick links

Citations

1 review citation

Inhibitors of Factor VIIa/tissue factor.
Shirk et al. (2007)
5 other articles

1 mention without citation

Factor VII deficiency: a novel missense variant and genotype-phenotype correlation in patients from Southern Italy.
Tiscia et al. (2017)