Crystal structure of PBP3 transpeptidase domain from E. coli

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Interaction Mode of the Novel Monobactam AIC499 Targeting Penicillin Binding Protein 3 of Gram-Negative Bacteria.

Freischem, S.Grimm, I.Lopez-Perez, A.Willbold, D.Klenke, B.Vuong, C.Dingley, A.J.Weiergraber, O.H.

(2021) Biomolecules 11

  • DOI: https://doi.org/10.3390/biom11071057
  • Primary Citation of Related Structures:  
    7ONK, 7ONN, 7ONO, 7ONW, 7ONX, 7ONY, 7ONZ

  • PubMed Abstract: 

    Novel antimicrobial strategies are urgently required because of the rising threat of multi drug resistant bacterial strains and the infections caused by them. Among the available target structures, the so-called penicillin binding proteins are of particular interest, owing to their good accessibility in the periplasmic space, and the lack of homologous proteins in humans, reducing the risk of side effects of potential drugs. In this report, we focus on the interaction of the innovative β-lactam antibiotic AIC499 with penicillin binding protein 3 (PBP3) from Escherichia coli and Pseudomonas aeruginosa . This recently developed monobactam displays broad antimicrobial activity, against Gram-negative strains, and improved resistance to most classes of β-lactamases. By analyzing crystal structures of the respective complexes, we were able to explore the binding mode of AIC499 to its target proteins. In addition, the apo structures determined for PBP3, from P. aeruginosa and the catalytic transpeptidase domain of the E. coli orthologue, provide new insights into the dynamics of these proteins and the impact of drug binding.

  • Organizational Affiliation

    Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, 52425 Jülich, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidoglycan D,D-transpeptidase FtsI410Escherichia coli K-12Mutation(s): 0 
Gene Names: ftsIpbpBb0084JW0082
Find proteins for P0AD68 (Escherichia coli (strain K12))
Explore P0AD68 
Go to UniProtKB:  P0AD68
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AD68
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on TMO

Download Ideal Coordinates CCD File 
B [auth A]trimethylamine oxide
C3 H9 N O
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.28α = 90
b = 109.28β = 90
c = 143.229γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
STARANISOdata processing

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release
  • Version 1.1: 2021-09-22
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description