› 7dem

X-ray diffraction
1.9Å resolution

Crystal structure of P.aeruginosa LpxC in complex with inhibitor

Released:
DOI: 10.2210/pdb7dem/pdb
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PDB entry 7dem coloured by chain, front view.
PDB entry 7dem coloured by chain, side view.
PDB entry 7dem coloured by chain, top view.
Source organism: Pseudomonas aeruginosa PAO1
Primary publication:
Lead optimization of 2-hydroxymethyl imidazoles as non-hydroxamate LpxC inhibitors: Discovery of TP0586532.
Ushiyama F, Takashima H, Matsuda Y, Ogata Y, Sasamoto N, Kurimoto-Tsuruta R, Ueki K, Tanaka-Yamamoto N, Endo M, Mima M, Fujita K, Takata I, Tsuji S, Yamashita H, Okumura H, Otake K, Sugiyama H
Bioorg Med Chem 30 115964 (2021)
PMID: 33385955

Function and Biology Details

Reaction catalysed: 
UDP-3-O-((3R)-3-hydroxyacyl)-N-acetyl-alpha-D-glucosamine + H(2)O = UDP-3-O-((3R)-3-hydroxyacyl)-alpha-D-glucosamine + acetate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155612 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
UDP-3-O-acyl-N-acetylglucosamine deacetylase Chain: A
Molecule details ›
Chain: A
Length: 299 amino acids
Theoretical weight: 33.15 KDa
Source organism: Pseudomonas aeruginosa PAO1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P47205 (Residues: 1-299; Coverage: 99%)
Gene names: PA4406, envA, lpxC
Sequence domains: UDP-3-O-acyl N-acetylglycosamine deacetylase

Ligands and Environments

2 bound ligands:
Ligand ZN 1 x ZN
Ligand H4O 1 x H4O
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P21
Unit cell:
a: 35.854Å b: 66.306Å c: 63.542Å
α: 90° β: 90.63° γ: 90°
R-values:
R R work R free
0.196 0.194 0.238
Expression system: Escherichia coli BL21(DE3)

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Citations

4 review citations

Structure- and Ligand-Dynamics-Based Design of Novel Antibiotics Targeting Lipid A Enzymes LpxC and LpxH in Gram-Negative Bacteria.
Zhou et al. (2021)
3 more

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