7ZED

Solution structure of thanatin-like derivative 7 in complex with E.coli LptA mutant Q62L


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


Literature

Peptidomimetic antibiotics disrupt the lipopolysaccharide transport bridge of drug-resistant Enterobacteriaceae.

Schuster, M.Brabet, E.Oi, K.K.Desjonqueres, N.Moehle, K.Le Poupon, K.Hell, S.Gable, S.Rithie, V.Dillinger, S.Zbinden, P.Luther, A.Li, C.Stiegeler, S.D'Arco, C.Locher, H.Remus, T.DiMaio, S.Motta, P.Wach, A.Jung, F.Upert, G.Obrecht, D.Benghezal, M.Zerbe, O.

(2023) Sci Adv 9: eadg3683-eadg3683

  • DOI: https://doi.org/10.1126/sciadv.adg3683
  • Primary Citation of Related Structures:  
    7QS6, 7ZAX, 7ZED, 8BSS

  • PubMed Abstract: 

    The rise of antimicrobial resistance poses a substantial threat to our health system, and, hence, development of drugs against novel targets is urgently needed. The natural peptide thanatin kills Gram-negative bacteria by targeting proteins of the lipopolysaccharide transport (Lpt) machinery. Using the thanatin scaffold together with phenotypic medicinal chemistry, structural data, and a target-focused approach, we developed antimicrobial peptides with drug-like properties. They exhibit potent activity against Enterobacteriaceae both in vitro and in vivo while eliciting low frequencies of resistance. We show that the peptides bind LptA of both wild-type and thanatin-resistant Escherichia coli and Klebsiella pneumoniae strains with low-nanomolar affinities. Mode of action studies revealed that the antimicrobial activity involves the specific disruption of the Lpt periplasmic protein bridge.


  • Organizational Affiliation

    University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipopolysaccharide export system protein LptA118Escherichia coli K-12Mutation(s): 1 
Gene Names: lptAyhbNb3200JW3167
UniProt
Find proteins for P0ADV1 (Escherichia coli (strain K12))
Explore P0ADV1 
Go to UniProtKB:  P0ADV1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADV1
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Thanatin-like derivative16Podisus maculiventrisMutation(s): 6 
UniProt
Find proteins for P55788 (Podisus maculiventris)
Explore P55788 
Go to UniProtKB:  P55788
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55788
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  4 Unique
IDChains TypeFormula2D DiagramParent
DAB
Query on DAB
B
L-PEPTIDE LINKINGC4 H10 N2 O2ALA
EU0
Query on EU0
B
L-PEPTIDE LINKINGC6 H14 N3 O2VAL
HYP
Query on HYP
B
L-PEPTIDE LINKINGC5 H9 N O3PRO
LE1
Query on LE1
B
L-PEPTIDE LINKINGC5 H11 N O2 SVAL
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
InnosuisseEuropean Union33285.1 IP-LS

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 2.0: 2023-06-14
    Changes: Atomic model, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 3.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations