› 1nl0

X-ray diffraction
2.2Å resolution

Crystal structure of human factor IX Gla domain in complex of an inhibitory antibody, 10C12

Released:
DOI: 10.2210/pdb1nl0/pdb
PDB entry 1nl0 coloured by chain, front view.
PDB entry 1nl0 coloured by chain, side view.
PDB entry 1nl0 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of the calcium-stabilized human factor IX Gla domain bound to a conformation-specific anti-factor IX antibody.
Huang M, Furie BC, Furie B
J Biol Chem 279 14338-46 (2004)
PMID: 14722079

Function and Biology Details

Reaction catalysed: 
Selective cleavage of Arg-|-Ile bond in factor X to form factor Xa.
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
hetero hexamer
Assembly name:
PDBe Complex ID:
PDB-CPX-208304 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
anti-factor IX antibody, 10C12, chain L Chain: L
Molecule details ›
Chain: L
Length: 213 amino acids
Theoretical weight: 22.63 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins
anti-factor IX antibody, 10C12, chain H Chain: H
Molecule details ›
Chain: H
Length: 224 amino acids
Theoretical weight: 23.8 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins
Coagulation factor IXa light chain Chain: G
Molecule details ›
Chain: G
Length: 51 amino acids
Theoretical weight: 7.12 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P00740 (Residues: 47-91; Coverage: 10%)
Gene name: F9
Sequence domains: Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain

Ligands and Environments

2 bound ligands:
Ligand SO4 1 x SO4
Ligand CA 6 x CA
1 modified residue:
Ligand CGU 18 x CGU

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: C2
Unit cell:
a: 105.089Å b: 71.614Å c: 90.867Å
α: 90° β: 119.14° γ: 90°
R-values:
R R work R free
0.235 0.233 0.27
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

9 review citations

Blood coagulation and its regulation by anticoagulant pathways: genetic pathogenesis of bleeding and thrombotic diseases.
Dahlbäck B. (2005)
8 more

11 mentions without citation

The Molecular Basis of FIX Deficiency in Hemophilia B.
Shen et al. (2022)
10 more