› 5ze6

X-ray diffraction
2.5Å resolution

CRYSTAL STRUCTURE OF OCTAPRENYL PYROPHOSPHATE SYNTHASE FROM ESCHERICHIA COLI WITH BPH-981

Released:
DOI: 10.2210/pdb5ze6/pdb
PDB 5ze6 coloured by chain and viewed from the front.
PDB 5ze6 coloured by chain and viewed from the side.
PDB 5ze6 coloured by chain and viewed from the top.
Source organism: Escherichia coli K-12
Primary publication:
Discovery of Lipophilic Bisphosphonates That Target Bacterial Cell Wall and Quinone Biosynthesis.
Malwal SR, Chen L, Hicks H, Qu F, Liu W, Shillo A, Law WX, Zhang J, Chandnani N, Han X, Zheng Y, Chen CC, Guo RT, AbdelKhalek A, Seleem MN, Oldfield E
J. Med. Chem. 62 2564-2581 (2019)
PMID: 30730737

Function and Biology Details

Reaction catalysed: 
(2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate = 5 diphosphate + all-trans-octaprenyl diphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Octaprenyl diphosphate synthase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 323 amino acids
Theoretical weight: 35.25 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0AD57 (Residues: 1-323; Coverage: 100%)
Gene names: JW3154, b3187, cel, ispB, yhbD
Sequence domains: Polyprenyl synthetase
Structure domains: Farnesyl Diphosphate Synthase

Ligands and Environments

2 bound ligands:
Ligand HJX 2 x HJX
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL13B1
Spacegroup: P212121
Unit cell:
a: 94.032Å b: 111.999Å c: 133.822Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.185 0.264
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

β-Lactams against the Fortress of the Gram-Positive Staphylococcus aureus Bacterium.
Fisher et al. (2021)
1 other article

1 mention without citation

Discovery of Lipophilic Bisphosphonates That Target Bacterial Cell Wall and Quinone Biosynthesis.
Malwal et al. (2019)