› 2hur

X-ray diffraction
1.62Å resolution

Escherichia coli nucleoside diphosphate kinase

Released:
DOI: 10.2210/pdb2hur/pdb
PDB entry 2hur coloured by chain, front view.
PDB entry 2hur coloured by chain, side view.
PDB entry 2hur coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
The structure of the Escherichia coli nucleoside diphosphate kinase reveals a new quaternary architecture for this enzyme family.
Moynié L, Giraud MF, Georgescauld F, Lascu I, Dautant A
Proteins 67 755-65 (2007)
PMID: 17330300

Function and Biology Details

Reaction catalysed: 
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
homo tetramer
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-141541 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleoside diphosphate kinase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 142 amino acids
Theoretical weight: 15.35 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A763 (Residues: 2-143; Coverage: 99%)
Gene names: JW2502, b2518, ndk
Sequence domains: Nucleoside diphosphate kinase
Structure domains: Nucleoside diphosphate kinase-like domain

Ligands and Environments

1 bound ligand:
Ligand SO4 6 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: C2
Unit cell:
a: 118.904Å b: 76.095Å c: 104.588Å
α: 90° β: 112.99° γ: 90°
R-values:
R R work R free
0.196 0.191 0.215
Expression system: Escherichia coli

Quick links

Citations

1 review citation

The mitochondrial nucleoside diphosphate kinase (NDPK-D/NME4), a moonlighting protein for cell homeostasis.
Lacombe et al. (2018)
13 other articles

5 mentions without citation

Structure, Folding and Stability of Nucleoside Diphosphate Kinases.
Georgescauld et al. (2020)
4 more