› 3ac9

X-ray diffraction
2.1Å resolution

Crystal structure of human NUDT5 complexed with 8-oxo-dGDP and manganese

Released:
DOI: 10.2210/pdb3ac9/pdb
PDB entry 3ac9 coloured by chain, front view.
PDB entry 3ac9 coloured by chain, side view.
PDB entry 3ac9 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Diverse substrate recognition and hydrolysis mechanisms of human NUDT5.
Arimori T, Tamaoki H, Nakamura T, Kamiya H, Ikemizu S, Takagi Y, Ishibashi T, Harashima H, Sekiguchi M, Yamagata Y
Nucleic Acids Res 39 8972-83 (2011)
PMID: 21768126

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:
  • not assigned
Cellular component:
  • not assigned
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: 195 amino acids
Theoretical weight: 21.64 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UKK9 (Residues: 14-208; Coverage: 89%)
Gene names: HSPC115, NUDIX5, NUDT5
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

2 bound ligands:
Ligand 8GD 2 x 8GD
Ligand MN 2 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: C2
Unit cell:
a: 113.24Å b: 40.442Å c: 99.418Å
α: 90° β: 121.59° γ: 90°
R-values:
R R work R free
0.197 0.195 0.236
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Evolution of Enzyme Kinetic Mechanisms.
Ulusu NN. (2015)
1 more

3 mentions without citation

Targeted NUDT5 inhibitors block hormone signaling in breast cancer cells.
Page et al. (2018)
2 more