› 1khz

X-ray diffraction
2.04Å resolution

Structure of the ADPR-ase in complex with AMPCPR and Mg

Released:
DOI: 10.2210/pdb1khz/pdb
PDB entry 1khz coloured by chain, front view.
PDB entry 1khz coloured by chain, side view.
PDB entry 1khz coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Mechanism of the Escherichia coli ADP-ribose pyrophosphatase, a Nudix hydrolase.
Gabelli SB, Bianchet MA, Ohnishi Y, Ichikawa Y, Bessman MJ, Amzel LM
Biochemistry 41 9279-85 (2002)
PMID: 12135348

Function and Biology Details

Reaction catalysed: 
ADP-D-ribose + H(2)O = AMP + D-ribose 5-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188087 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
ADP-ribose pyrophosphatase Chains: A, B
Molecule details ›
Chains: A, B
Length: 209 amino acids
Theoretical weight: 23.7 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: Q93K97 (Residues: 1-209; Coverage: 100%)
Gene names: JW3002, aspP, b3034, nudF, yqiE, yzzG
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

3 bound ligands:
Ligand CL 1 x CL
Ligand MG 3 x MG
Ligand ADV 1 x ADV
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P212121
Unit cell:
a: 67.1Å b: 67.4Å c: 96.5Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.196 0.257
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Structures and mechanisms of Nudix hydrolases.
Mildvan et al. (2005)
3 more

27 mentions without citation

Recent Advances in Multilayer-Structure Dielectrics for Energy Storage Application.
Feng et al. (2021)
26 more