› 2aer

X-ray diffraction
1.87Å resolution

Crystal Structure of Benzamidine-Factor VIIa/Soluble Tissue Factor complex.

Released:
DOI: 10.2210/pdb2aer/pdb
PDB entry 2aer coloured by chain, front view.
PDB entry 2aer coloured by chain, side view.
PDB entry 2aer coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
High resolution structures of p-aminobenzamidine- and benzamidine-VIIa/soluble tissue factor: unpredicted conformation of the 192-193 peptide bond and mapping of Ca2+, Mg2+, Na+, and Zn2+ sites in factor VIIa.
Bajaj SP, Schmidt AE, Agah S, Bajaj MS, Padmanabhan K
J Biol Chem 281 24873-88 (2006)
PMID: 16757484

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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140352 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Factor VII light chain Chain: L
Molecule details ›
Chain: L
Length: 142 amino acids
Theoretical weight: 16.36 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P08709 (Residues: 61-202; Coverage: 32%)
Gene name: F7
Sequence domains:
Factor VII heavy chain Chain: H
Molecule details ›
Chain: H
Length: 254 amino acids
Theoretical weight: 28.1 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P08709 (Residues: 213-466; Coverage: 57%)
Gene name: F7
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Tissue factor Chain: T
Molecule details ›
Chain: T
Length: 206 amino acids
Theoretical weight: 23.37 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P13726 (Residues: 38-242; Coverage: 78%)
Gene name: F3
Sequence domains:
Structure domains: Immunoglobulins

Ligands and Environments

8 bound ligands:
Ligand GLC 1 x GLC
Ligand FUC 1 x FUC
Ligand MG 3 x MG
Ligand CA 6 x CA
Ligand NA 1 x NA
Ligand ZN 2 x ZN
Ligand CL 3 x CL
Ligand BEN 1 x BEN
1 modified residue:
Ligand CGU 10 x CGU

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-3
Spacegroup: P212121
Unit cell:
a: 69.9Å b: 81.2Å c: 125.9Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.191 0.191 0.256

Quick links

Citations

13 review citations

Thrombin.
Di Cera E. (2008)
12 more

2 mentions without citation

Structural biology of factor VIIa/tissue factor initiated coagulation.
Vadivel et al. (2012)
1 more