9G3S | pdb_00009g3s

LecB from Pseudomonas aeruginosa in complex with a synthetic thiofucoside

PDB DOI: https://doi.org/10.2210/pdb9G3S/pdb

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

Deposited: 2024-07-12 Released: 2024-11-27
Deposition Author(s): Melicher, F., Faltinek, L., Wimmerova, M.
Funding Organization(s): Ministry of Education, Youth and Sports of the Czech Republic

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.219 (Depositor), 0.206 (DCC)
R-Value Work:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 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.

(2025) Chemistry 31: e202403546-e202403546

PubMed: 39535852 Search on PubMed
DOI: https://doi.org/10.1002/chem.202403546
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 99.56 kDa
Atom Count: 7,177
Modeled Residue Count: 912
Deposited Residue Count: 912
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucose-binding lectin PA-IIL	A, B, C, D, E A, B, C, D, E, F, G, H	114	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: lecB, PA3361
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HYN5
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-1)-1-thio-beta-D-galactopyranose	I, K, L, M, N I, K, L, M, N, O, P	2	N/A	N/A	Interactions Focus chain I Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Interactions & Density Focus chain I Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
1-thio-beta-D-galactopyranose-(1-1)-alpha-L-fucopyranose	J	2	N/A	N/A	Interactions Focus chain J Interactions & Density Focus chain J

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain XA [auth G] SDF format, chain X [auth B] SDF format, chain UA [auth F] SDF format, chain U [auth A] SDF format, chain TA [auth F] SDF format, chain T [auth A] SDF format, chain SA [auth F] SDF format, chain S [auth A] SDF format, chain PA [auth E] SDF format, chain OA [auth E] SDF format, chain NA [auth E] SDF format, chain MA [auth E] SDF format, chain LA [auth E] SDF format, chain IA [auth D] SDF format, chain FA [auth C] SDF format, chain EA [auth C] SDF format, chain DB [auth H] SDF format, chain DA [auth C] SDF format, chain CB [auth H] SDF format, chain CA [auth C] SDF format, chain BB [auth H] SDF format, chain BA [auth C] SDF format, chain AB [auth H] MOL2 format, chain Y [auth B] MOL2 format, chain XA [auth G] MOL2 format, chain X [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain U [auth A] MOL2 format, chain TA [auth F] MOL2 format, chain T [auth A] MOL2 format, chain SA [auth F] MOL2 format, chain S [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain OA [auth E] MOL2 format, chain NA [auth E] MOL2 format, chain MA [auth E] MOL2 format, chain LA [auth E] MOL2 format, chain IA [auth D] MOL2 format, chain FA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain DB [auth H] MOL2 format, chain DA [auth C] MOL2 format, chain CB [auth H] MOL2 format, chain CA [auth C] MOL2 format, chain BB [auth H] MOL2 format, chain BA [auth C] MOL2 format, chain AB [auth H] mmCIF format, chain Y [auth B] mmCIF format, chain XA [auth G] mmCIF format, chain X [auth B] mmCIF format, chain UA [auth F] mmCIF format, chain U [auth A] mmCIF format, chain TA [auth F] mmCIF format, chain T [auth A] mmCIF format, chain SA [auth F] mmCIF format, chain S [auth A] mmCIF format, chain PA [auth E] mmCIF format, chain OA [auth E] mmCIF format, chain NA [auth E] mmCIF format, chain MA [auth E] mmCIF format, chain LA [auth E] mmCIF format, chain IA [auth D] mmCIF format, chain FA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain DB [auth H] mmCIF format, chain DA [auth C] mmCIF format, chain CB [auth H] mmCIF format, chain CA [auth C] mmCIF format, chain BB [auth H] mmCIF format, chain BA [auth C] mmCIF format, chain AB [auth H]	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		Interactions Focus chain AB [auth H] Focus chain BA [auth C] Focus chain BB [auth H] Focus chain CA [auth C] Focus chain CB [auth H] Focus chain DA [auth C] Focus chain DB [auth H] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain IA [auth D] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain S [auth A] Focus chain SA [auth F] Focus chain T [auth A] Focus chain TA [auth F] Focus chain U [auth A] Focus chain UA [auth F] Focus chain X [auth B] Focus chain XA [auth G] Focus chain Y [auth B] Interactions & Density Focus chain AB [auth H] Focus chain BA [auth C] Focus chain BB [auth H] Focus chain CA [auth C] Focus chain CB [auth H] Focus chain DA [auth C] Focus chain DB [auth H] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain IA [auth D] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain S [auth A] Focus chain SA [auth F] Focus chain T [auth A] Focus chain TA [auth F] Focus chain U [auth A] Focus chain UA [auth F] Focus chain X [auth B] Focus chain XA [auth G] Focus chain Y [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain ZA [auth H] SDF format, chain Z [auth C] SDF format, chain YA [auth H] SDF format, chain WA [auth G] SDF format, chain W [auth B] SDF format, chain VA [auth G] SDF format, chain V [auth B] SDF format, chain RA [auth F] SDF format, chain R [auth A] SDF format, chain QA [auth F] SDF format, chain Q [auth A] SDF format, chain KA [auth E] SDF format, chain JA [auth E] SDF format, chain HA [auth D] SDF format, chain GA [auth D] SDF format, chain AA [auth C] MOL2 format, chain ZA [auth H] MOL2 format, chain Z [auth C] MOL2 format, chain YA [auth H] MOL2 format, chain WA [auth G] MOL2 format, chain W [auth B] MOL2 format, chain VA [auth G] MOL2 format, chain V [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth F] MOL2 format, chain Q [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain HA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain AA [auth C] mmCIF format, chain ZA [auth H] mmCIF format, chain Z [auth C] mmCIF format, chain YA [auth H] mmCIF format, chain WA [auth G] mmCIF format, chain W [auth B] mmCIF format, chain VA [auth G] mmCIF format, chain V [auth B] mmCIF format, chain RA [auth F] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth F] mmCIF format, chain Q [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain JA [auth E] mmCIF format, chain HA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain AA [auth C]	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		Interactions Focus chain AA [auth C] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain Q [auth A] Focus chain QA [auth F] Focus chain R [auth A] Focus chain RA [auth F] Focus chain V [auth B] Focus chain VA [auth G] Focus chain W [auth B] Focus chain WA [auth G] Focus chain YA [auth H] Focus chain Z [auth C] Focus chain ZA [auth H] Interactions & Density Focus chain AA [auth C] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain Q [auth A] Focus chain QA [auth F] Focus chain R [auth A] Focus chain RA [auth F] Focus chain V [auth B] Focus chain VA [auth G] Focus chain W [auth B] Focus chain WA [auth G] Focus chain YA [auth H] Focus chain Z [auth C] Focus chain ZA [auth H]