7BFY

Structure of the apo form of the N terminal domain of Bc2L-C lectin (1-131)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


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Literature

Prediction and Validation of a Druggable Site on Virulence Factor of Drug Resistant Burkholderia cenocepacia.

Lal, K.Bermeo, R.Cramer, J.Vasile, F.Ernst, B.Bernardi, A.Belvisi, L.Varrot, A.Imberty, A.

(2021) Chemistry 

  • DOI: 10.1002/chem.202100252
  • Primary Citation of Related Structures:  
    6ZZW, 7BFY

  • PubMed Abstract: 
  • Burkholderia cenocepacia is an opportunistic gram-negative bacterium that causes infections in patients suffering from chronic granulomatous diseases and cystic fibrosis. It displays significant morbidity and mortality due to extreme resistance to almost all clinically useful antibiotics ...

    Burkholderia cenocepacia is an opportunistic gram-negative bacterium that causes infections in patients suffering from chronic granulomatous diseases and cystic fibrosis. It displays significant morbidity and mortality due to extreme resistance to almost all clinically useful antibiotics. The bacterial lectin BC2L-C expressed in B. cenocepacia is an interesting drug target involved in bacterial adhesion and subsequent deadly infection to the host. We solved the first high resolution crystal structure of the apo form of the lectin N-terminal domain (BC2L-C-nt) and compared it with the ones complexed with carbohydrate ligands. Virtual screening of a small fragment library identified potential hits predicted to bind in the vicinity of the fucose binding site. A series of biophysical techniques and a X-ray crystallographic screening were employed to validate the interaction of the hits with the protein domain. The X-ray structure of BC2L-C-nt complexed with one of the identified active fragments confirmed the ability of the site computationally identified to host drug-like fragments. The fragment affinity could be determined by titration microcalorimetry. These structure-based strategies further provide an opportunity to elaborate the fragments into high affinity anti-adhesive glycomimetics, as therapeutic agents against B. cenocepacia.


    Organizational Affiliation

    CERMAV, Glycobiologie Moleculaire, BP 53, 38041, Grenoble, FRANCE.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lectin A131Burkholderia cenocepacia J2315Mutation(s): 0 
Gene Names: BCAM0185
Find proteins for B4EH86 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610))
Explore B4EH86 
Go to UniProtKB:  B4EH86
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.987α = 90
b = 42.987β = 90
c = 94.678γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



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: 2021-04-07
    Type: Initial release