9G3S

LecB from Pseudomonas aeruginosa in complex with a synthetic thiofucoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.185 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Bispecific Thio-linked Disaccharides as Inhibitors of Pseudomonas aeruginosa Lectins LecA (PA-IL) and LecB (PA-IIL): Dual-Targeting Strategy.

Faltinek, L.Melicher, F.Kelemen, V.Mezo, E.Borbas, A.Wimmerova, M.

(2024) Chemistry : e202403546-e202403546

  • DOI: https://doi.org/10.1002/chem.202403546
  • Primary Citation of Related Structures:  
    9G3R, 9G3S

  • PubMed Abstract: 

    Pseudomonas aeruginosa is a prevalent opportunistic human pathogen, particularly associated with cystic fibrosis. Among its virulence factors are the LecA and LecB lectins. Both lectins play an important role in the adhesion to the host cells and display cytotoxic activity. In this study, we successfully synthesized hardly hydrolysable carbohydrate ligands targeting these pathogenic lectins, including two bispecific glycans. The interactions between LecA/LecB lectins and synthetic glycans were evaluated using hemagglutination (yeast agglutination) inhibition assays, comparing their efficacy with corresponding monosaccharides. Additionally, the binding affinities of bispecific glycans were assessed using isothermal titration calorimetry (ITC). Structural insight into the lectin-ligand interaction was obtained by determining the crystal structures of LecA/LecB lectins in complex with one of the bispecific ligands using X ray crystallography. This comprehensive investigation into the inhibitory potential of synthetic glycosides against P. aeruginosa lectins sheds light on their potential application in antimicrobial therapy.


  • Organizational Affiliation

    Masaryk University: Masarykova Univerzita, Faculty of Science, CZECHIA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fucose-binding lectin PA-IIL
A, B, C, D, E
A, B, C, D, E, F, G, H
114Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: lecBPA3361
UniProt
Find proteins for Q9HYN5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HYN5 
Go to UniProtKB:  Q9HYN5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HYN5
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-1)-1-thio-beta-D-galactopyranose
I, K, L, M, N
I, K, L, M, N, O, P
2N/AN/A
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
1-thio-beta-D-galactopyranose-(1-1)-alpha-L-fucopyranose
J
2N/AN/A
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AB [auth H]
BA [auth C]
BB [auth H]
CA [auth C]
CB [auth H]
AB [auth H],
BA [auth C],
BB [auth H],
CA [auth C],
CB [auth H],
DA [auth C],
DB [auth H],
EA [auth C],
FA [auth C],
IA [auth D],
LA [auth E],
MA [auth E],
NA [auth E],
OA [auth E],
PA [auth E],
S [auth A],
SA [auth F],
T [auth A],
TA [auth F],
U [auth A],
UA [auth F],
X [auth B],
XA [auth G],
Y [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth C]
GA [auth D]
HA [auth D]
JA [auth E]
KA [auth E]
AA [auth C],
GA [auth D],
HA [auth D],
JA [auth E],
KA [auth E],
Q [auth A],
QA [auth F],
R [auth A],
RA [auth F],
V [auth B],
VA [auth G],
W [auth B],
WA [auth G],
YA [auth H],
Z [auth C],
ZA [auth H]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.488α = 90
b = 96.951β = 90
c = 128.68γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLM2023042

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release