8ONU | pdb_00008onu

Solution structure of thanatin analogue 7 in complex with LptAm(Ab)1.0


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

Validation slider image for 8ONU

This is version 2.1 of the entry. See complete history

Literature

Early Molecular Insights into Thanatin Analogues Binding to A. baumannii LptA.

Oi, K.K.Moehle, K.Schuster, M.Zerbe, O.

(2023) Molecules 28

  • DOI: https://doi.org/10.3390/molecules28114335
  • Primary Citation Related Structures: 
    8ONU

  • PubMed Abstract: 

    The cationic antimicrobial ß-hairpin, thanatin, was recently developed into drug-like analogues active against carbapenem-resistant Enterobacteriaceae (CRE). The analogues represent new antibiotics with a novel mode of action targeting LptA in the periplasm and disrupting LPS transport. The compounds lose antimicrobial efficacy when the sequence identity to E. coli LptA falls below 70%. We wanted to test the thanatin analogues against LptA of a phylogenetic distant organism and investigate the molecular determinants of inactivity. Acinetobacter baumannii ( A. baumannii ) is a critical Gram-negative pathogen that has gained increasing attention for its multi-drug resistance and hospital burden. A. baumannii LptA shares 28% sequence identity with E. coli LptA and displays an intrinsic resistance to thanatin and thanatin analogues (MIC values > 32 µg/mL) through a mechanism not yet described. We investigated the inactivity further and discovered that these CRE-optimized derivatives can bind to LptA of A. baumannii in vitro, despite the high MIC values. Herein, we present a high-resolution structure of A. baumannii LptAm in complex with a thanatin derivative 7 and binding affinities of selected thanatin derivatives. Together, these data offer structural insights into why thanatin derivatives are inactive against A. baumannii LptA, despite binding events in vitro.


  • Organizational Affiliation
    • Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 16.27 kDa 
  • Atom Count: 1,139 
  • Modeled Residue Count: 149 
  • Deposited Residue Count: 149 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lipopolysaccharide export system protein LptA133Acinetobacter baumanniiMutation(s): 0 
Gene Names: 
UniProt
Find proteins for V5VEZ9 (Acinetobacter baumannii)
Explore V5VEZ9 
Go to UniProtKB:  V5VEZ9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV5VEZ9
Sequence Annotations
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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
4FO
Query on 4FO
B
D-PEPTIDE LINKINGC4 H10 N2 O2

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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: 2023-06-14
    Type: Initial release
  • Version 1.1: 2023-06-21
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2023-11-29
    Changes: Database references