X-ray diffraction
2.6Å resolution

Structure of nucleoside diphosphate kinase 2 with bound dGTP from Arabidopsis


Function and Biology Details

Reaction catalysed:
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Entry contents:
1 distinct polypeptide molecule
Nucleoside diphosphate kinase II, chloroplastic Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 153 amino acids
Theoretical weight: 17.08 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
  • Canonical: O64903 (Residues: 79-231; Coverage: 66%)
Gene names: At5g63310, MDC12.28, NDPK2
Sequence domains: Nucleoside diphosphate kinase
Structure domains: Nucleoside diphosphate kinase-like domain

Ligands and Environments

2 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 6B
Spacegroup: P212121
Unit cell:
a: 69.035Å b: 108.52Å c: 118.316Å
α: 90° β: 90° γ: 90°
R R work R free
0.209 0.207 0.282
Expression system: Escherichia coli BL21(DE3)