› 8v9i

X-ray diffraction
1.98Å resolution

1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Deinococcus radiodurans with D-phenylalanine-derived triazole acetylphosphonate (D-PheTrAP) bound

Released:
DOI: 10.2210/pdb8v9i/pdb
PDB entry 8v9i coloured by chain, front view.
PDB entry 8v9i coloured by chain, side view.
PDB entry 8v9i coloured by chain, top view.
Source organism: Deinococcus radiodurans
Primary publication:
Potent Inhibition of E. coli DXP Synthase by a gem-Diaryl Bisubstrate Analog.
Coco LB, Toci EM, Chen PY, Drennan CL, Freel Meyers CL
ACS Infect Dis 10 1312-1326 (2024)
PMID: 38513073

Function and Biology Details

Reaction catalysed: 
Pyruvate + D-glyceraldehyde 3-phosphate = 1-deoxy-D-xylulose 5-phosphate + CO(2)
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-576968 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
1-deoxy-D-xylulose-5-phosphate synthase Chains: A, B
Molecule details ›
Chains: A, B
Length: 650 amino acids
Theoretical weight: 70.03 KDa
Source organism: Deinococcus radiodurans
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9RUB5 (Residues: 1-629; Coverage: 100%)
Gene names: DR_1475, dxs
Sequence domains:

Ligands and Environments

4 bound ligands:
Ligand A1AAN 2 x A1AAN
Ligand MG 2 x MG
Ligand NA 2 x NA
Ligand BGQ 1 x BGQ
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 78.616Å b: 125.321Å c: 152.017Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.161 0.16 0.181
Expression system: Escherichia coli

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