› 4h3c

X-ray diffraction
1.93Å resolution

Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-987

Released:
DOI: 10.2210/pdb4h3c/pdb
PDB entry 4h3c coloured by chain, front view.
PDB entry 4h3c coloured by chain, side view.
PDB entry 4h3c coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Antibacterial drug leads targeting isoprenoid biosynthesis.
Zhu W, Zhang Y, Sinko W, Hensler ME, Olson J, Molohon KJ, Lindert S, Cao R, Li K, Wang K, Wang Y, Liu YL, Sankovsky A, de Oliveira CA, Mitchell DA, Nizet V, McCammon JA, Oldfield E
Proc Natl Acad Sci U S A 110 123-8 (2013)
PMID: 23248302

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-548358 (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
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 0YZ 3 x 0YZ
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P212121
Unit cell:
a: 63.333Å b: 69.103Å c: 111.686Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.206 0.25
Expression system: Escherichia coli

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Citations

12 review citations

Computational methods in drug discovery.
Leelananda et al. (2016)
11 more

2 mentions without citation

Antibacterial drug leads targeting isoprenoid biosynthesis.
Zhu et al. (2013)
1 more