Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52.53 kDa 
• Atom Count: 3937 
• Modelled Residue Count: 484 
• Deposited Residue Count: 484 
• Unique protein chains: 1

4A6S

Structure of the PAIL lectin from Pseudomonas aeruginosa in complex with 2-Naphtyl-1-thio-beta-D-galactopyranoside

• DOI: 10.2210/pdb4A6S/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-11-08 Released: 2012-10-17 
• Deposition Author(s): Rodrigue, J., Ganne, G., Blanchard, B., Saucier, C., Giguere, D., Chiao, T.S., Varrot, A., Imberty, A., Roy, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.259 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 

Literature

Aromatic Thioglycoside Inhibitors Against the Virulence Factor Leca from Pseudomonas Aeruginosa.

Rodrigue, J., Ganne, G., Blanchard, B., Saucier, C., Giguere, D., Shiao, T.C., Varrot, A., Imberty, A., Roy, R.

(2013) Org Biomol Chem 11: 6906

• PubMed: 24057051 
• DOI: 10.1039/c3ob41422a
• Primary Citation of Related Structures:  
  4A6S


• PubMed Abstract: 
  

Three small families of hydrolytically stable thioaryl glycosides were prepared as inhibitors of the LecA (PA-IL) virulence factor corresponding to the carbohydrate binding lectin from the bacterial pathogen Pseudomonas aeruginosa. The monosaccharidic arylthio β-d-galactopyranosides served as a common template for the major series that was also substituted at the O-3 position. Arylthio disaccharides from lactose and from melibiose constituted the other two series members. In spite of the fact that the natural ligand for LecA is a glycolipid of the globotriaosylceramide having an α-d-galactopyranoside epitope, this study illustrated that the β-d-galactopyranoside configuration having a hydrophobic aglycon could override the requirement toward the anomeric configuration of the natural sugar. The enzyme linked lectin assay together with isothermal titration microcalorimetry established that naphthyl 1-thio-β-d-galactopyranoside () gave the best inhibition with an IC50 twenty-three times better than that of the reference methyl α-d-galactopyranoside. In addition it showed a KD of 6.3 μM which was ten times better than that of the reference compound. The X-ray crystal structure of LecA with was also obtained.

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Organizational Affiliation: 

PharmaQAM - Department of Chemistry, Université du Québec à Montréal, P.O. Box 8888, Succ. Centre-ville, Montréal, Québec, Canada H3C 3P8. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PA-I GALACTOPHILIC LECTIN	A, B, C, D	121	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: lecA, pa1L, PA2570
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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GS9 (Subject of Investigation/LOI)	F [auth A], H [auth B], J [auth C], L [auth D]	naphthalen-2-yl 1-thio-beta-D-galactopyranoside C16 H18 O5 S UTPJJZURVZIAID-CWVYHPPDSA-N
CA	E [auth A], G [auth B], I [auth C], K [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GS9	PDBBind:  4A6S	Kd: 6300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.259 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.334	α = 90
b = 54.334	β = 90
c = 390.501	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2011-11-08 
• Released Date: 2012-10-17 
Deposition Author(s): Rodrigue, J., Ganne, G., Blanchard, B., Saucier, C., Giguere, D., Chiao, T.S., Varrot, A., Imberty, A., Roy, R.

Revision History  

• Version 1.0: 2012-10-17
  Type: Initial release
  
• Version 1.1: 2012-11-14
  Changes: Atomic model, Other
• Version 1.2: 2013-10-02
  Changes: Database references
• Version 1.3: 2013-10-09
  Changes: Database references
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Derived calculations, Other, Structure summary