› 3th2

X-ray diffraction
1.72Å resolution

Mg2+ Is Required for Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla) Domains of Vitamin K-Dependent Clotting Factors At Physiological Ca2+

Released:
DOI: 10.2210/pdb3th2/pdb
PDB entry 3th2 coloured by chain, front view.
PDB entry 3th2 coloured by chain, side view.
PDB entry 3th2 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Vadivel K, Agah S, Cascio D, Padmanabhan K, Bajaj SP

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 (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: 205 amino acids
Theoretical weight: 23.3 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P13726 (Residues: 38-242; Coverage: 78%)
Gene name: F3
Sequence domains:
Structure domains: Immunoglobulins

Ligands and Environments

7 bound ligands:
Ligand BGC 1 x BGC
Ligand FUC 1 x FUC
Ligand MG 3 x MG
Ligand CA 6 x CA
Ligand BEN 1 x BEN
Ligand NA 1 x NA
Ligand CL 2 x CL
1 modified residue:
Ligand CGU 10 x CGU

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: P212121
Unit cell:
a: 69.94Å b: 80.874Å c: 126.43Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.191 0.189 0.233

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