› 3l85

X-ray diffraction
2.3Å resolution

Crystal structure of human NUDT5 complexed with 8-oxo-dGMP

Released:
DOI: 10.2210/pdb3l85/pdb
PDB entry 3l85 coloured by chain, front view.
PDB entry 3l85 coloured by chain, side view.
PDB entry 3l85 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

1 bound ligand:
Ligand 8OG 2 x 8OG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: C2
Unit cell:
a: 112.655Å b: 40.008Å c: 98.47Å
α: 90° β: 121.53° γ: 90°
R-values:
R R work R free
0.217 0.215 0.261
Expression system: Escherichia coli

Quick links

Citations

2 review citations

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

2 mentions without citation

Diverse substrate recognition and hydrolysis mechanisms of human NUDT5.
Arimori et al. (2011)
1 more