› 3q89

X-ray diffraction
2.9Å resolution

Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with CDP

Released:
DOI: 10.2210/pdb3q89/pdb
PDB entry 3q89 coloured by chain, front view.
PDB entry 3q89 coloured by chain, side view.
PDB entry 3q89 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

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-177189 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleoside diphosphate kinase Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
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

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

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: C2
Unit cell:
a: 186.613Å b: 73.055Å c: 102.272Å
α: 90° β: 108.23° γ: 90°
R-values:
R R work R free
0.254 0.252 0.293
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

2 mentions without citation

Isotope-Labeled RNA Building Blocks for NMR Structure and Dynamics Studies.
Olenginski et al. (2021)
1 more