PDBe 5knc

X-ray diffraction
3.02Å resolution

Crystal structure of the 3 ADP-bound V1 complex

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
V-type sodium ATPase subunit B Chains: D, E, F
Molecule details ›
Chains: D, E, F
Length: 465 amino acids
Theoretical weight: 51.72 KDa
Source organism: Enterococcus hirae ATCC 9790
Expression system: Escherichia coli
UniProt:
  • Canonical: Q08637 (Residues: 1-458; Coverage: 100%)
Gene names: EHR_08265, ntpB
Sequence domains:
Structure domains: Rossmann fold
V-type sodium ATPase subunit D Chain: G
Molecule details ›
Chain: G
Length: 217 amino acids
Theoretical weight: 25.12 KDa
Source organism: Enterococcus hirae ATCC 9790
Expression system: Escherichia coli
UniProt:
  • Canonical: P43435 (Residues: 1-210; Coverage: 100%)
Gene names: EHR_08270, ntpD
Sequence domains: ATP synthase subunit D
V-type sodium ATPase subunit G Chain: H
Molecule details ›
Chain: H
Length: 115 amino acids
Theoretical weight: 12.69 KDa
Source organism: Enterococcus hirae ATCC 9790
Expression system: Escherichia coli
UniProt:
  • Canonical: P43455 (Residues: 1-103; Coverage: 100%)
Gene names: EHR_08255, ntpG, ntpQ
Sequence domains: ATP synthase (F/14-kDa) subunit
Structure domains: ATPase, V1 complex, subunit F
V-type sodium ATPase catalytic subunit A Chains: A, B, C

Ligands and Environments


No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-1A
Spacegroup: P212121
Unit cell:
a: 121.68Å b: 126.49Å c: 225.26Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.214 0.253
Expression system: Escherichia coli