4AUJ | pdb_00004auj

FimH lectin domain co-crystal with a alpha-D-mannoside O-linked to para hydroxypropargyl phenyl

• PDB DOI: https://doi.org/10.2210/pdb4AUJ/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Escherichia coli UTI89
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-05-17 Released: 2013-05-29 
• Deposition Author(s): Bouckaert, J., Touaibia, M., Roos, G., Shiao, T.C., Wang, Q., Papadopoulos, A., Roy, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.185 (Depositor), 0.178 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Validation of Reactivity Descriptors to Assess the Aromatic Stacking within the Tyrosine Gate of Fimh.

Roos, G., Wellens, A., Touaibia, M., Yamakawa, N., Geerlings, P., Roy, R., Wyns, L., Bouchaert, J.

(2013) ACS Med Chem Lett 4: 1085

• PubMed: 24900609 
• DOI: https://doi.org/10.1021/ml400269v
• Primary Citation Related Structures: 
  4ATT, 4AUJ, 4BUQ


• PubMed Abstract: 
  

  Antagonists of the FimH adhesin, a protein almost universally present at the extremity of type-1 fimbriae expressed by Escherichia coli, have been abundantly in the spotlight as alternative treatments of urinary tract infections. The antagonists function as bacterial antiadhesives through highly specific α-d-mannose binding in a charged and polar pocket at the tip of the FimH lectin domain and by the stacking of alkyl or aromatic moieties substituted on the mannose with two tyrosine residues (Tyr48 and Tyr137) at the entrance of the mannose-binding pocket. Using high-resolution crystal data, interaction energies are calculated for the different observed aromatic stacking modes between the tyrosines and the antagonist. The dispersion component of the interaction energy correlates with the observed electron density. The quantum chemical reactivity descriptors local hardness and polarizability were successfully validated as prediction tools for ligand affinity in the tyrosine gate of FimH and therefore have potential for rapid drug screening.

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Organizational Affiliation: 
• General Chemistry, Vrije Universiteit Brussel, Structural Biology Brussels, VIB and Vrije Universiteit Brussel, and Brussels Center for Redox Biology, Pleinlaan 2, 1050 Brussels, Belgium ; General Chemistry, Vrije Universiteit Brussel, Structural Biology Brussels, VIB and Vrije Universiteit Brussel, and Brussels Center for Redox Biology, Pleinlaan 2, 1050 Brussels, Belgium ; General Chemistry, Vrije Universiteit Brussel, Structural Biology Brussels, VIB and Vrije Universiteit Brussel, and Brussels Center for Redox Biology, Pleinlaan 2, 1050 Brussels, Belgium.
General Chemistry, Vrije Universiteit Brussel, Structural Biology Brussels, VIB and Vrije Universiteit Brussel, and Brussels Center for Redox Biology, Pleinlaan 2, 1050 Brussels, Belgium.
Department of Chemistry, Université du Québec à Montréal , Montréal, QC H3C 3P8, Canada ; Department of Chemistry and Biochemistry, Université de Moncton , Moncton, NB E1A 3E9, Canada.
Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 du CNRS, Université Lille 1 , 59655 Villeneuve d'Ascq, France.
Department of Chemistry, Université du Québec à Montréal , Montréal, QC H3C 3P8, Canada.
General Chemistry, Vrije Universiteit Brussel, Structural Biology Brussels, VIB and Vrije Universiteit Brussel, and Brussels Center for Redox Biology, Pleinlaan 2, 1050 Brussels, Belgium ; Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 du CNRS, Université Lille 1 , 59655 Villeneuve d'Ascq, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 17.23 kDa 
• Atom Count: 1,452 
• Modeled Residue Count: 158 
• Deposited Residue Count: 158 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FIMH	A	158	Escherichia coli UTI89	Mutation(s): 0
UniProt
Find proteins for P08191 (Escherichia coli (strain K12)) Explore P08191  Go to UniProtKB:  P08191

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HNW	B [auth A]	4-(3-hydroxyprop-1-yn-1-yl)phenyl alpha-D-mannopyranoside C15 H18 O7 GNTPQQUJBAFHOR-MRLBHPIUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.185 (Depositor), 0.178 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.92	α = 90
b = 42.29	β = 90
c = 96.34	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-29 
Deposition Author(s): Bouckaert, J., Touaibia, M., Roos, G., Shiao, T.C., Wang, Q., Papadopoulos, A., Roy, R.

Revision History  

• Version 1.0: 2013-05-29
  Type: Initial release
  
• Version 1.1: 2013-12-25
  Changes: Database references
• Version 1.2: 2014-06-18
  Changes: Database references
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Derived calculations, Other, Structure summary
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.5: 2024-05-08
  Changes: Data collection
• Version 1.6: 2024-10-23
  Changes: Structure summary