7Z62 | pdb_00007z62

Structure of the LecA lectin from Pseudomonas aeruginosa in complex with a biaryl-thiogalactoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 
    0.206 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.178 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery of potent 1,1-diarylthiogalactoside glycomimetic inhibitors of Pseudomonas aeruginosa LecA with antibiofilm properties.

Bruneau, A.Gillon, E.Furiga, A.Brachet, E.Alami, M.Roques, C.Varrot, A.Imberty, A.Messaoudi, S.

(2022) Eur J Med Chem 247: 115025-115025

  • DOI: https://doi.org/10.1016/j.ejmech.2022.115025
  • Primary Citation Related Structures: 
    7Z62, 7Z63

  • PubMed Abstract: 

    In this work, β-thiogalactoside mimetics bearing 1,1-diarylmethylene or benzophenone aglycons have been prepared and assayed for their affinity towards LecA, a lectin and virulence factor from Pseudomonas aeruginosa involved in bacterial adhesion and biofilm formation. The hit compound presents higher efficiency than previously described monovalent inhibitors and the crystal structure confirmed the occurrence of additional contacts between the aglycone and the protein surface. The highest affinity (160 nM) was obtained for a divalent ligand containing two galactosides. The monovalent high affinity compound (K d  = 1 μM) obtained through structure-activity relationship (SAR) showed efficient antibiofilm activity with no associated bactericidal activity.


  • Organizational Affiliation
    • BioCIS, Univ. Paris-Sud, CNRS, University Paris-Saclay, Châtenay-Malabry, France.

Macromolecule Content 

  • Total Structure Weight: 26.15 kDa 
  • Atom Count: 2,297 
  • Modeled Residue Count: 242 
  • Deposited Residue Count: 242 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PA-I galactophilic lectinA [auth AAA],
B [auth BBB]
121Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: lecApa1LPA2570
UniProt
Find proteins for Q05097 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q05097 
Go to UniProtKB:  Q05097
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05097
Sequence Annotations
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Reference Sequence

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
IEC BindingDB:  7Z62 Kd: 3000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free:  0.206 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.178 (DCC) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.122α = 90
b = 57.089β = 90
c = 83.399γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2023-01-18 
  • Deposition Author(s): Varrot, A.

Funding OrganizationLocationGrant Number
Centre National de la Recherche Scientifique (CNRS)France--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-18
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description