› 4bc5

X-ray diffraction
1.98Å resolution

Crystal structure of human D-xylulokinase in complex with inhibitor 5- deoxy-5-fluoro-D-xylulose

Released:
DOI: 10.2210/pdb4bc5/pdb
PDB entry 4bc5 coloured by chain, front view.
PDB entry 4bc5 coloured by chain, side view.
PDB entry 4bc5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure and function of human xylulokinase, an enzyme with important roles in carbohydrate metabolism.
Bunker RD, Bulloch EM, Dickson JM, Loomes KM, Baker EN
J Biol Chem 288 1643-52 (2013)
PMID: 23179721

Function and Biology Details

Reaction catalysed: 
ATP + D-xylulose = ADP + D-xylulose 5-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130881 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Xylulose kinase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 538 amino acids
Theoretical weight: 58.57 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O75191 (Residues: 1-536; Coverage: 100%)
Gene name: XYLB
Sequence domains:
Structure domains: Nucleotidyltransferase; domain 5

Ligands and Environments

2 bound ligands:
Ligand 5FX 3 x 5FX
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P32
Unit cell:
a: 102.109Å b: 102.109Å c: 159.101Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.173 0.172 0.192
Expression system: Escherichia coli BL21(DE3)

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Citations

2 review citations

Assessing and maximizing data quality in macromolecular crystallography.
Karplus et al. (2015)
1 more

3 mentions without citation

Structure and function of human xylulokinase, an enzyme with important roles in carbohydrate metabolism.
Bunker et al. (2013)
2 more