7ONW | pdb_00007onw

Crystal structure of PBP3 from E. coli in complex with AIC499


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.271 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.236 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

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 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.

Macromolecule Content 

  • Total Structure Weight: 62.2 kDa 
  • Atom Count: 3,593 
  • Modeled Residue Count: 485 
  • Deposited Residue Count: 564 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidoglycan D,D-transpeptidase FtsI564Escherichia coli K-12Mutation(s): 0 
Gene Names: ftsIpbpBb0084JW0082
EC: 3.4.16.4
UniProt
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
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VL5
(Subject of Investigation/LOI)

Query on VL5



Download:Ideal Coordinates CCD File
B [auth A](2S)-2-[(Z)-[1-(2-azanyl-1,3-thiazol-4-yl)-2-[[(2S)-3-methyl-1-oxidanylidene-3-(sulfooxyamino)butan-2-yl]amino]-2-oxidanylidene-ethylidene]amino]oxy-3-[4-[N-[(3R)-piperidin-3-yl]carbamimidoyl]phenoxy]propanoic acid
C25 H34 N8 O10 S2
NFNVPYWCKFTXAX-OOLKDPNPSA-N
MPD

Query on MPD



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.271 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.904α = 90
b = 106.904β = 90
c = 285.83γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
STARANISOdata scaling

Structure Validation

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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
  • Version 1.3: 2024-10-23
    Changes: Structure summary