› 6g9f

X-ray diffraction
2.35Å resolution

Structural basis for the inhibition of E. coli PBP2

Released:
DOI: 10.2210/pdb6g9f/pdb
PDB entry 6g9f coloured by chain, front view.
PDB entry 6g9f coloured by chain, side view.
PDB entry 6g9f coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Structural Basis for E. coli Penicillin Binding Protein (PBP) 2 Inhibition, a Platform for Drug Design.
Levy N, Bruneau JM, Le Rouzic E, Bonnard D, Le Strat F, Caravano A, Chevreuil F, Barbion J, Chasset S, Ledoussal B, Moreau F, Ruff M
J Med Chem 62 4742-4754 (2019)
PMID: 30995398

Function and Biology Details

Reaction catalysed: 
Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-142334 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptidoglycan D,D-transpeptidase MrdA Chain: A
Molecule details ›
Chain: A
Length: 561 amino acids
Theoretical weight: 62.81 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P0AD65 (Residues: 57-615; Coverage: 88%)
Gene names: JW0630, b0635, mrdA, pbpA
Sequence domains:

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-X
Spacegroup: C2221
Unit cell:
a: 125.078Å b: 182.875Å c: 74.767Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.201 0.199 0.248
Expression system: Escherichia coli BL21

Quick links

Citations

4 review citations

Fighting antibiotic resistance-strategies and (pre)clinical developments to find new antibacterials.
Walesch et al. (2023)
3 more

2 mentions without citation

Structural Characterization of Diazabicyclooctane β-Lactam "Enhancers" in Complex with Penicillin-Binding Proteins PBP2 and PBP3 of Pseudomonas aeruginosa.
Rajavel et al. (2021)
1 more