› 9bvk

Electron Microscopy
3.6Å resolution

Vitamin K-dependent gamma-carboxylase with factor IX propeptide and glutamate-rich region and with vitamin K hydroquinone

Released:
DOI: 10.2210/pdb9bvk/pdb
PDB entry 9bvk coloured by chain, front view.
PDB entry 9bvk coloured by chain, side view.
PDB entry 9bvk coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Li W, Liu B, Cao Q
Related structures: EMD-44935

Function and Biology Details

Reactions catalysed: 
[Peptidyl]-4-carboxyglutamate + 2,3-epoxyphylloquinone + H(2)O = [peptidyl]-glutamate + CO(2) + O(2) + phylloquinol
Selective cleavage of Arg-|-Ile bond in factor X to form factor Xa.
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-284163 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Vitamin K-dependent gamma-carboxylase Chain: A
Molecule details ›
Chain: A
Length: 732 amino acids
Theoretical weight: 85.01 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P38435 (Residues: 27-758; Coverage: 97%)
Gene names: GC, GGCX
Sequence domains:
Coagulation factor IXa light chain Chain: P
Molecule details ›
Chain: P
Length: 64 amino acids
Theoretical weight: 7.8 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P00740 (Residues: 29-92; Coverage: 15%)
Gene name: F9
Sequence domains: Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
3 bound ligands:
Ligand A1AVC 1 x A1AVC
Ligand 6PL 2 x 6PL
Ligand NAG 1 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.6Å
Relevant EMDB volumes: EMD-44935
Expression system: Homo sapiens

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