› 6mv4

X-ray diffraction
1.37Å resolution

CRYSTAL STRUCTURE OF HUMAN COAGULATION FACTOR IXa

Released:
DOI: 10.2210/pdb6mv4/pdb
PDB entry 6mv4 coloured by chain, front view.
PDB entry 6mv4 coloured by chain, side view.
PDB entry 6mv4 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Sodium-site in serine protease domain of human coagulation factor IXa: evidence from the crystal structure and molecular dynamics simulations study.
Vadivel K, Schreuder HA, Liesum A, Schmidt AE, Goldsmith G, Bajaj SP
J Thromb Haemost 17 574-584 (2019)
PMID: 30725510

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:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-524060 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Coagulation factor IXa heavy chain Chain: H
Molecule details ›
Chain: H
Length: 235 amino acids
Theoretical weight: 26.19 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P00740 (Residues: 227-461; Coverage: 54%)
Gene name: F9
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Coagulation factor IXa light chain Chain: L
Molecule details ›
Chain: L
Length: 54 amino acids
Theoretical weight: 5.94 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P00740 (Residues: 132-185; Coverage: 13%)
Gene name: F9
Sequence domains: Coagulation Factor Xa inhibitory site
Structure domains: Laminin

Ligands and Environments

7 bound ligands:
Ligand SO4 6 x SO4
Ligand EDO 2 x EDO
Ligand FMT 1 x FMT
Ligand PBZ 1 x PBZ
Ligand CA 1 x CA
Ligand NA 1 x NA
Ligand CL 3 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-3
Spacegroup: I4122
Unit cell:
a: 109.758Å b: 109.758Å c: 112.458Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.178 0.177 0.21
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Surface loops of trypsin-like serine proteases as determinants of function.
Goettig et al. (2019)
7 other articles

5 mentions without citation

Sodium-site in serine protease domain of human coagulation factor IXa: evidence from the crystal structure and molecular dynamics simulations study.
Vadivel et al. (2019)
4 more