5ABZ

Complex of the FimH lectin with a C-linked naphtyl alpha-D-mannoside in soaked trigonal crystals at 2.40 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.135 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structures of C-Mannosylated Anti-Adhesives Bound to the Type 1 Fimbrial Fimh Adhesin

De Ruyck, J.Lensink, M.F.Bouckaert, J.

(2016) Iucrj 3: 163

  • DOI: 10.1107/S2052252516002487
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Selective inhibitors of the type 1 fimbrial adhesin FimH are recognized as attractive alternatives for antibiotic therapies and prophylaxes against Escherichia coli infections such as urinary-tract infections. To construct these inhibitors, the α-d-m ...

    Selective inhibitors of the type 1 fimbrial adhesin FimH are recognized as attractive alternatives for antibiotic therapies and prophylaxes against Escherichia coli infections such as urinary-tract infections. To construct these inhibitors, the α-d-mannopyranoside of high-mannose N-glycans, recognized with exclusive specificity on glycoprotein receptors by FimH, forms the basal structure. A hydrophobic aglycon is then linked to the mannose by the O1 oxygen inherently present in the α-anomeric configuration. Substitution of this O atom by a carbon introduces a C-glycosidic bond, which may enhance the therapeutic potential of such compounds owing to the inability of enzymes to degrade C-glycosidic bonds. Here, the first crystal structures of the E. coli FimH adhesin in complex with C-glycosidically linked mannopyranosides are presented. These findings explain the role of the spacer in positioning biphenyl ligands for interactions by means of aromatic stacking in the tyrosine gate of FimH and how the normally hydrated C-glycosidic link is tolerated. As these new compounds can bind FimH, it can be assumed that they have the potential to serve as potent new antagonists of FimH, paving the way for the design of a new family of anti-adhesive compounds against urinary-tract infections.


    Organizational Affiliation

    Université Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle , 59000 Lille, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FIMH
A, B
158Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: fimH
Find proteins for P08191 (Escherichia coli (strain K12))
Go to UniProtKB:  P08191
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download SDF File 
Download CCD File 
A, B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Z47
Query on Z47

Download SDF File 
Download CCD File 
A, B
(2R,3S,4R,5S,6R)-2-(HYDROXYMETHYL)-6-[3-(NAPHTHALEN-1-YL)PROPYL]OXANE-3,4,5-TRIOL
C19 H24 O5
RCVLTURVGCLYEX-BRIYLRKRSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.135 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 90.830α = 90.00
b = 90.830β = 90.00
c = 79.870γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-05-18
    Type: Database references
  • Version 2.0: 2019-10-23
    Type: Atomic model, Data collection, Other