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X-ray diffraction
1.8Å resolution

Structure of Arabidopsis thaliana Ribokinase complexed with Ribose and ATP

Released:
DOI: 10.2210/pdb6ils/pdb
Model geometry
Fit model/data
PDB entry 6ils coloured by chain, front view.
PDB entry 6ils coloured by chain, side view.
PDB entry 6ils coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Crystal structure and mutational analyses of ribokinase from Arabidopsis thaliana.
Kang PA, Oh J, Lee H, Witte CP, Rhee S
J Struct Biol 206 110-118 (2019)
PMID: 30822455

Function and Biology Details

Reaction catalysed: 
ATP + D-ribose = ADP + D-ribose 5-phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-106545 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribokinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 313 amino acids
Theoretical weight: 32.93 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A1A6H3 (Residues: 68-379; Coverage: 82%)
Gene names: At1g17160, F20D23.14, RBSK
Sequence domains: pfkB family carbohydrate kinase
Structure domains: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase

Ligands and Environments

3 bound ligands:
Ligand ATP 2 x ATP
Ligand NA 2 x NA
Ligand RIB 1 x RIB
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PAL/PLS BEAMLINE 7A (6B, 6C1)
Spacegroup: P42212
Unit cell:
a: 99.46Å b: 99.46Å c: 165.74Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.218 0.216 0.251
Expression system: Escherichia coli BL21(DE3)

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Citations

6 citation in other articles

Structural basis for the substrate specificity and catalytic features of pseudouridine kinase from Arabidopsis thaliana.
Kim et al. (2021)
5 more