› 2dsc

X-ray diffraction
2Å resolution

Crystal structure of human ADP-ribose pyrophosphatase NUDT5 in complex with magnesium and ADP-ribose

Released:
DOI: 10.2210/pdb2dsc/pdb
PDB entry 2dsc coloured by chain, front view.
PDB entry 2dsc coloured by chain, side view.
PDB entry 2dsc coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structures of human NUDT5 reveal insights into the structural basis of the substrate specificity.
Zha M, Zhong C, Peng Y, Hu H, Ding J
J Mol Biol 364 1021-33 (2006)
PMID: 17052728

Function and Biology Details

Reactions catalysed: 
ATP + D-ribose 5-phosphate = diphosphate + ADP-D-ribose
ADP-D-ribose + H(2)O = AMP + D-ribose 5-phosphate
8-oxo-GDP + H(2)O = 8-oxo-GMP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193850 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
ADP-sugar pyrophosphatase Chains: A, B
Molecule details ›
Chains: A, B
Length: 212 amino acids
Theoretical weight: 23.39 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9UKK9 (Residues: 1-210; Coverage: 96%)
Gene names: HSPC115, NUDIX5, NUDT5
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand APR 2 x APR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44B2
Spacegroup: C2
Unit cell:
a: 112.466Å b: 40.623Å c: 99.685Å
α: 90° β: 121.44° γ: 90°
R-values:
R R work R free
0.193 0.193 0.228
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Role of the NUDT Enzymes in Breast Cancer.
Wright et al. (2021)
21 other articles

11 mentions without citation

Insight into the machinery that oils chromatin dynamics.
Wright et al. (2016)
10 more