› 6r2w

X-ray diffraction
1.25Å resolution

Crystal structure of the super-active FVIIa variant VYT in complex with tissue factor

Released:
DOI: 10.2210/pdb6r2w/pdb
PDB entry 6r2w coloured by chain, front view.
PDB entry 6r2w coloured by chain, side view.
PDB entry 6r2w coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Beating tissue factor at its own game: Design and properties of a soluble tissue factor-independent coagulation factor VIIa.
Sorensen AB, Tuneew I, Svensson LA, Persson E, Østergaard H, Overgaard MT, Olsen OH, Gandhi PS
J Biol Chem 295 517-528 (2020)
PMID: 31801825

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 analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140352 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 distinct):
Factor VII light chain Chain: L
Molecule details ›
Chain: L
Length: 143 amino acids
Theoretical weight: 16.49 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P08709 (Residues: 61-203; Coverage: 32%)
Gene name: F7
Sequence domains:
Factor VII heavy chain Chain: H
Molecule details ›
Chain: H
Length: 249 amino acids
Theoretical weight: 27.51 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P08709 (Residues: 213-466; Coverage: 56%)
Gene name: F7
Sequence domains: Trypsin
Tissue factor Chain: T
Molecule details ›
Chain: T
Length: 210 amino acids
Theoretical weight: 23.76 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P13726 (Residues: 33-242; Coverage: 80%)
Gene name: F3
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: BGC, XYS
Carbohydrate polymer
4 bound ligands:
Ligand CA 9 x CA
Ligand FUC 1 x FUC
Ligand TMA 10 x TMA
Ligand 0Z7 1 x 0Z7
1 modified residue:
Ligand CGU 10 x CGU

Experiments and Validation Details

Entry percentile scores
X-ray source: MAX II BEAMLINE I911-3
Spacegroup: P212121
Unit cell:
a: 71.31Å b: 80.04Å c: 123.38Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.171 0.17 0.194
Expression systems:
  • Cricetulus griseus
  • Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Biochemical, molecular and clinical aspects of coagulation factor VII and its role in hemostasis and thrombosis.
Bernardi et al. (2021)
2 more

4 mentions without citation

Beating tissue factor at its own game: Design and properties of a soluble tissue factor-independent coagulation factor VIIa.
Sorensen et al. (2020)
3 more