› 3q83

X-ray diffraction
2.5Å resolution

Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase

Released:
DOI: 10.2210/pdb3q83/pdb
PDB entry 3q83 coloured by chain, front view.
PDB entry 3q83 coloured by chain, side view.
PDB entry 3q83 coloured by chain, top view.
Source organism: Staphylococcus aureus subsp. aureus COL
Primary publication:
Conformational basis for substrate recognition and regulation of catalytic activity in Staphylococcus aureus nucleoside di-phosphate kinase.
Srivastava SK, Rajasree K, Gopal B
Biochim Biophys Acta 1814 1349-57 (2011)
PMID: 21745603

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 trimer (preferred)
homo hexamer
Assembly name:
PDBe Complex ID:
PDB-CPX-177190 (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: 157 amino acids
Theoretical weight: 17.66 KDa
Source organism: Staphylococcus aureus subsp. aureus COL
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5HFV4 (Residues: 1-149; Coverage: 100%)
Gene names: SACOL1509, ndk
Sequence domains: Nucleoside diphosphate kinase
Structure domains: Nucleoside diphosphate kinase-like domain

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: P3221
Unit cell:
a: 91.615Å b: 91.615Å c: 176.876Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.215 0.213 0.269
Expression system: Escherichia coli

Quick links

Citations

6 citation in other articles

Reconstruction and Characterization of Thermally Stable and Catalytically Active Proteins Comprising an Alphabet of ~ 13 Amino Acids.
Kimura et al. (2020)
5 more

1 mention without citation

Pathogen and human NDPK-proteins promote AML cell survival via monocyte NLRP3-inflammasome activation.
Trova et al. (2023)