› 1s59

X-ray diffraction
2.6Å resolution

Structure of nucleoside diphosphate kinase 2 with bound dGTP from Arabidopsis

Released:
DOI: 10.2210/pdb1s59/pdb
PDB entry 1s59 coloured by chain, front view.
PDB entry 1s59 coloured by chain, side view.
PDB entry 1s59 coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Structural analysis of Arabidopsis thaliana nucleoside diphosphate kinase-2 for phytochrome-mediated light signaling.
Im YJ, Kim JI, Shen Y, Na Y, Han YJ, Kim SH, Song PS, Eom SH
J Mol Biol 343 659-70 (2004)
PMID: 15465053

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130283 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
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)
UniProt:
  • 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:
Ligand DGI 1 x DGI
Ligand DGT 1 x DGT
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-values:
R R work R free
0.209 0.207 0.282
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Histidine kinases and the missing phosphoproteome from prokaryotes to eukaryotes.
Adam et al. (2018)
1 more