Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 52.27 kDa 
• Atom Count: 4436 
• Residue Count: 484 
• Unique protein chains: 1

5D21

Multivalency Effects in Glycopeptide Dendrimer Inhibitors of Pseudomonas aeruginosa Biofilms Targeting Lectin LecA

• DOI: 10.2210/pdb5D21/pdb

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


• Deposited: 2015-08-05 Released: 2015-11-25 
• Deposition Author(s): Bergmann, M., Michaud, G., Visini, R., Jin, X., Stocker, A., Darbre, T., Reymond, J.-L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.225 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 

Literature

Multivalency effects on Pseudomonas aeruginosa biofilm inhibition and dispersal by glycopeptide dendrimers targeting lectin LecA.

Bergmann, M., Michaud, G., Visini, R., Jin, X., Gillon, E., Stocker, A., Imberty, A., Darbre, T., Reymond, J.L.

(2016) Org Biomol Chem 14: 138-148

• PubMed: 26416170 
• DOI: 10.1039/c5ob01682g
• Primary Citation of Related Structures:  
  5D21


• PubMed Abstract: 
  

The galactose specific lectin LecA partly mediates the formation of antibiotic resistant biofilms by Pseudomonas aeruginosa, an opportunistic pathogen causing lethal airways infections in immunocompromised and cystic fibrosis patients, suggesting that preventing LecA binding to natural saccharides might provide new opportunities for treatment. Here 8-fold (G3) and 16-fold (G4) galactosylated analogs of GalAG2, a tetravalent G2 glycopeptide dendrimer LecA ligand and P. aeruginosa biofilm inhibitor, were obtained by convergent chloroacetyl thioether (ClAc) ligation between 4-fold or 8-fold chloroacetylated dendrimer cores and digalactosylated dendritic arms. Hemagglutination inhibition, isothermal titration calorimetry and biofilm inhibition assays showed that G3 dendrimers bind LecA slightly better than their parent G2 dendrimers and induce complete biofilm inhibition and dispersal of P. aeruginosa biofilms, while G4 dendrimers show reduced binding and no biofilm inhibition. A binding model accounting for the observed saturation of glycopeptide dendrimer galactosyl groups and LecA binding sites is proposed based on the crystal structure of a G3 dendrimer LecA complex.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LecA	A, B, C, D	121	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: lecA, pa1L, ERS445055_02484, PA257_2995, PA8380_27900, PAE221_02397, PAMH19_6043, YQ19_15530
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
56N	A, B, C, D	phenyl beta-D-galactopyranoside C12 H16 O6 NEZJDVYDSZTRFS-YBXAARCKSA-N
CA	A, B, C, D	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.225 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.539	α = 117.51
b = 72.94	β = 104.9
c = 79.008	γ = 89.91

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-08-05 
• Released Date: 2015-11-25 
Deposition Author(s): Bergmann, M., Michaud, G., Visini, R., Jin, X., Stocker, A., Darbre, T., Reymond, J.-L.

Revision History 

• Version 1.0: 2015-11-25
  Type: Initial release
  
• Version 1.1: 2015-12-23
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations