Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 48.77 kDa 
• Atom Count: 4129 
• Modelled Residue Count: 456 
• Deposited Residue Count: 456 
• Unique protein chains: 1

5A3O

Crystal structure of the LecB lectin from Pseudomonas aeruginosa in complex with Methyl 6-(cinnamido)-6-deoxy-alpha-D-mannopyranoside at 1.6 ansgtrom

• PDB DOI: 10.2210/pdb5A3O/pdb

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


• Deposited: 2015-06-02 Released: 2015-07-22 
• Deposition Author(s): Sommer, R., Hauck, D., Varrot, A., Audfray, A., Imberty, A., Titz, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.204 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 

Literature

Cinnamide Derivatives of D-Mannose as Inhibitors of the Bacterial Virulence Factor Lecb from Pseudomonas Aeruginosa

Sommer, R., Hauck, D., Varrot, A., Wagner, S., Audfray, A., Prestel, A., Moleer, H.M., Imberty, A., Titz, A.

(2015) ChemistryOpen 4: 756

• PubMed: 27308201 
• DOI: 10.1002/open.201500162
• Primary Citation of Related Structures:  
  5A3O


• PubMed Abstract: 
  

Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen with high antibiotic resistance. Its lectin LecB was identified as a virulence factor and is relevant in bacterial adhesion and biofilm formation. Inhibition of LecB with carbohydrate-based ligands results in a decrease in toxicity and biofilm formation. We recently discovered two classes of potent drug-like glycomimetic inhibitors, that is, sulfonamides and cinnamides of d-mannose. Here, we describe the chemical synthesis and biochemical evaluation of more than 20 derivatives with increased potency compared to the unsubstituted cinnamide. The structure-activity relationship (SAR) obtained and the extended biophysical characterization allowed the experimental determination of the binding mode of these cinnamides with LecB. The established surface binding mode now allows future rational structure-based drug design. Importantly, all glycomimetics tested showed extended receptor residence times with half-lives in the 5-20 min range, a prerequisite for therapeutic application. Thus, the glycomimetics described here provide an excellent basis for future development of anti-infectives against this multidrug-resistant pathogen.

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Organizational Affiliation: 

Chemical Biology of Carbohydrates Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Universitätsstrasse 1066123 Saarbrücken Germany; Department of Chemistry and Graduate School Chemical Biology University of Konstanz 78457 KonstanzGermany; Deutsches Zentrum für Infektionsforschung (DZIF) Inhoffenstraße 738124 Braunschweig Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FUCOSE-BINDING LECTIN PA-IIL	A, B, C, D	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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MMA	G [auth A], L [auth B], Q [auth C], V [auth D]	methyl alpha-D-mannopyranoside C7 H14 O6 HOVAGTYPODGVJG-VEIUFWFVSA-N
DH6	H [auth A], M [auth B], R [auth C], W [auth D]	CINNAMIDE C9 H9 N O APEJMQOBVMLION-VOTSOKGWSA-N
CA	E [auth A], F [auth A], J [auth B], K [auth B], O [auth C], P [auth C], T [auth D], U [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	I [auth A], N [auth B], S [auth C], X [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.204 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.954	α = 101.8
b = 51.111	β = 99.4
c = 52.348	γ = 115.95

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-06-02 
• Released Date: 2015-07-22 
Deposition Author(s): Sommer, R., Hauck, D., Varrot, A., Audfray, A., Imberty, A., Titz, A.

Revision History  

• Version 1.0: 2015-07-22
  Type: Initial release
  
• Version 1.1: 2016-06-29
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary