7OLW | pdb_00007olw

Structure of the N-terminal domain of BC2L-C lectin (1-131) in complex with a synthetic beta-N-fucoside ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 
    0.129 (Depositor), 0.139 (DCC) 
  • R-Value Work: 
    0.103 (Depositor), 0.112 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Targeting a Multidrug-Resistant Pathogen: First Generation Antagonists of Burkholderia cenocepacia 's BC2L-C Lectin.

Bermeo, R.Lal, K.Ruggeri, D.Lanaro, D.Mazzotta, S.Vasile, F.Imberty, A.Belvisi, L.Varrot, A.Bernardi, A.

(2022) ACS Chem Biol 17: 2899-2910

  • DOI: https://doi.org/10.1021/acschembio.2c00532
  • Primary Citation Related Structures: 
    7OLU, 7OLW

  • PubMed Abstract: 

    Multidrug-resistant pathogens such as Burkholderia cenocepacia have become a hazard in the context of healthcare-associated infections, especially for patients admitted with cystic fibrosis or immuno-compromising conditions. Like other opportunistic Gram-negative bacteria, this pathogen establishes virulence and biofilms through lectin-mediated adhesion. In particular, the superlectin BC2L-C is believed to cross-link human epithelial cells to B. cenocepacia during pulmonary infections. We aimed to obtain glycomimetic antagonists able to inhibit the interaction between the N -terminal domain of BC2L-C (BC2L-C-Nt) and its target fucosylated human oligosaccharides. In a previous study, we identified by fragment virtual screening and validated a small set of molecular fragments that bind BC2L-C-Nt in the vicinity of the fucose binding site. Here, we report the rational design and synthesis of bifunctional C - or N -fucosides, generated by connecting these fragments to a fucoside core using a panel of rationally selected linkers. A modular route starting from two key fucoside intermediates was implemented for the synthesis, followed by evaluation of the new compounds as BC2L-C-Nt ligands with a range of techniques (surface plasmon resonance, isothermal titration calorimetry, saturation transfer difference NMR, differential scanning calorimetry, and X-ray crystallography). This study resulted in a hit molecule with an order of magnitude gain over the starting methyl fucoside and in two crystal structures of antagonist/lectin complexes.


  • Organizational Affiliation
    • CNRS, CERMAV, Univ. Grenoble Alpes, Grenoble 38000, France.

Macromolecule Content 

  • Total Structure Weight: 14.36 kDa 
  • Atom Count: 1,226 
  • Modeled Residue Count: 134 
  • Deposited Residue Count: 134 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LectinA [auth AAA]134Burkholderia cenocepacia J2315Mutation(s): 0 
Gene Names: BCAM0185
UniProt
Find proteins for B4EH86 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610))
Explore B4EH86 
Go to UniProtKB:  B4EH86
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4EH86
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VJW
(Subject of Investigation/LOI)

Query on VJW



Download:Ideal Coordinates CCD File
B [auth AAA]5-(3-aminophenyl)furan-2-carboxamido-(beta-L-fucopyranose)
C17 H20 N2 O6
QWRWVIPPQRQFMW-VUBKLASDSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free:  0.129 (Depositor), 0.139 (DCC) 
  • R-Value Work:  0.103 (Depositor), 0.112 (DCC) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.931α = 90
b = 42.931β = 90
c = 94.882γ = 120
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


Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionFrance765581

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-01
    Type: Initial release
  • Version 1.1: 2022-11-30
    Changes: Database references, Derived calculations
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description