› 2dxd

X-ray diffraction
1.77Å resolution

Crystal structure of nucleoside diphosphate kinase in complex with ATP analog

Released:
DOI: 10.2210/pdb2dxd/pdb
PDB entry 2dxd coloured by chain, front view.
PDB entry 2dxd coloured by chain, side view.
PDB entry 2dxd coloured by chain, top view.
Source organism: Pyrococcus horikoshii OT3
Entry authors: Kato-Murayama M, Murayama K, Terada T, Shirouzu M, Yokoyama S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
homo hexamer (preferred)
homo dodecamer
Assembly name:
PDBe Complex ID:
PDB-CPX-129724 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleoside diphosphate kinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 160 amino acids
Theoretical weight: 18.34 KDa
Source organism: Pyrococcus horikoshii OT3
Expression system: Escherichia coli
UniProt:
  • Canonical: O58429 (Residues: 1-157; Coverage: 100%)
Gene names: PH0698, ndk
Sequence domains: Nucleoside diphosphate kinase
Structure domains: Nucleoside diphosphate kinase-like domain

Ligands and Environments

2 bound ligands:
Ligand CL 2 x CL
Ligand AMP 2 x AMP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: R32
Unit cell:
a: 115.622Å b: 115.622Å c: 194.171Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.169 0.169 0.193
Expression system: Escherichia coli

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