3hrd

X-ray diffraction
2.2Å resolution

Crystal structure of nicotinate dehydrogenase

Released:
Source organism: Eubacterium barkeri
Primary publication:
The Mo-Se active site of nicotinate dehydrogenase.
Proc Natl Acad Sci U S A 106 11055-60 (2009)
PMID: 19549881

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
PDBe Complex ID:
PDB-CPX-171095 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Nicotinate dehydrogenase large molybdopterin subunit Chains: A, E
Molecule details ›
Chains: A, E
Length: 425 amino acids
Theoretical weight: 46.55 KDa
Source organism: Eubacterium barkeri
UniProt:
  • Canonical: Q0QLF2 (Residues: 1-425; Coverage: 100%)
Gene name: ndhL
Sequence domains:
Structure domains: Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
Nicotinate dehydrogenase medium molybdopterin subunit Chains: B, F
Molecule details ›
Chains: B, F
Length: 330 amino acids
Theoretical weight: 34.51 KDa
Source organism: Eubacterium barkeri
UniProt:
  • Canonical: Q0QLF1 (Residues: 1-330; Coverage: 100%)
Gene name: ndhM
Sequence domains: Molybdopterin cofactor-binding domain
Structure domains: Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
Nicotinate dehydrogenase FAD-subunit Chains: C, G
Molecule details ›
Chains: C, G
Length: 296 amino acids
Theoretical weight: 32.66 KDa
Source organism: Eubacterium barkeri
UniProt:
  • Canonical: Q0QLF4 (Residues: 1-296; Coverage: 100%)
Gene name: ndhF
Sequence domains:
Structure domains: CO dehydrogenase flavoprotein, C-terminal domain
Nicotinate dehydrogenase small FeS subunit Chains: D, H
Molecule details ›
Chains: D, H
Length: 160 amino acids
Theoretical weight: 16.99 KDa
Source organism: Eubacterium barkeri
UniProt:
  • Canonical: Q0QLF3 (Residues: 1-157; Coverage: 100%)
Gene name: ndhS
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand MCN 2 x MCN

Cofactor: Ligand FAD 2 x FAD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ENRAF-NONIUS FR591
Spacegroup: P21
Unit cell:
a: 97.069Å b: 71.7Å c: 214.485Å
α: 90° β: 90.23° γ: 90°
R-values:
R R work R free
0.224 0.213 0.251