› 3wyj

X-ray diffraction
2.1Å resolution

Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-789

Released:
DOI: 10.2210/pdb3wyj/pdb
PDB entry 3wyj coloured by chain, front view.
PDB entry 3wyj coloured by chain, side view.
PDB entry 3wyj coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Antibacterial drug leads: DNA and enzyme multitargeting.
Zhu W, Wang Y, Li K, Gao J, Huang CH, Chen CC, Ko TP, Zhang Y, Guo RT, Oldfield E
J Med Chem 58 1215-27 (2015)
PMID: 25574764

Function and Biology Details

Reaction catalysed: 
(2E,6E)-farnesyl diphosphate + 8 isopentenyl diphosphate = 8 diphosphate + di-trans,octa-cis-undecaprenyl diphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158013 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) Chains: A, B
Molecule details ›
Chains: A, B
Length: 253 amino acids
Theoretical weight: 28.48 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P60472 (Residues: 1-253; Coverage: 100%)
Gene names: JW0169, b0174, ispU, rth, uppS, yaeS
Sequence domains: Putative undecaprenyl diphosphate synthase
Structure domains: Decaprenyl diphosphate synthase-like

Ligands and Environments

1 bound ligand:
Ligand H78 1 x H78
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL13B1
Spacegroup: P212121
Unit cell:
a: 63.712Å b: 68.995Å c: 108.885Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.2 0.241
Expression system: Escherichia coli

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Citations

15 citation in other articles

Pentamidine sensitizes Gram-negative pathogens to antibiotics and overcomes acquired colistin resistance.
Stokes et al. (2017)
14 more

1 mention without citation

Antibacterial drug leads: DNA and enzyme multitargeting.
Zhu et al. (2015)