› 4xf6

X-ray diffraction
2.08Å resolution

myo-inositol 3-kinase bound with its products (ADP and 1D-myo-inositol 3-phosphate)

Released:
DOI: 10.2210/pdb4xf6/pdb
PDB entry 4xf6 coloured by chain, front view.
PDB entry 4xf6 coloured by chain, side view.
PDB entry 4xf6 coloured by chain, top view.
Source organism: Thermococcus kodakarensis KOD1
Primary publication:
Crystal Structure and Product Analysis of an Archaeal myo-Inositol Kinase Reveal Substrate Recognition Mode and 3-OH Phosphorylation.
Nagata R, Fujihashi M, Sato T, Atomi H, Miki K
Biochemistry 54 3494-503 (2015)
PMID: 25972008

Function and Biology Details

Reaction catalysed: 
ATP + myo-inositol = ADP + 1D-myo-inositol 3-phosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-177266 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Carbohydrate/pyrimidine kinase, PfkB family Chains: A, B
Molecule details ›
Chains: A, B
Length: 273 amino acids
Theoretical weight: 30.34 KDa
Source organism: Thermococcus kodakarensis KOD1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5JDA3 (Residues: 1-273; Coverage: 100%)
Gene name: TK2285
Structure domains: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase

Ligands and Environments

6 bound ligands:
Ligand LIP 2 x LIP
Ligand ADP 2 x ADP
Ligand INS 2 x INS
Ligand MG 2 x MG
Ligand IOD 15 x IOD
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: P212121
Unit cell:
a: 77.364Å b: 81.255Å c: 82.046Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.205 0.203 0.25
Expression system: Escherichia coli

Quick links

Citations

1 review citation

An overview of 25 years of research on Thermococcus kodakarensis, a genetically versatile model organism for archaeal research.
Rashid et al. (2020)
3 other articles