› 1u8w

X-ray diffraction
2.4Å resolution

Crystal structure of Arabidopsis thaliana nucleoside diphosphate kinase 1

Released:
DOI: 10.2210/pdb1u8w/pdb
PDB entry 1u8w coloured by chain, front view.
PDB entry 1u8w coloured by chain, side view.
PDB entry 1u8w 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:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153853 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleoside diphosphate kinase 1 Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 149 amino acids
Theoretical weight: 16.52 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P39207 (Residues: 1-149; Coverage: 100%)
Gene names: At4g09320, NDK1, NDPK1, T30A10.80
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: PAL/PLS BEAMLINE 6B
Spacegroup: P212121
Unit cell:
a: 73.935Å b: 96.319Å c: 134.703Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.227 0.281
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