Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Hetero 4-mer - A2B2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 25.51 kDa 
• Atom Count: 1840 
• Modelled Residue Count: 240 
• Deposited Residue Count: 240 
• Unique protein chains: 3

5D2A

Bifunctional dendrimers

• PDB DOI: 10.2210/pdb5D2A/pdb

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


• Deposited: 2015-08-05 Released: 2016-02-10 
• Deposition Author(s): Michaud, G., Visini, R., Stocker, A., Darbre, T., Reymond, J.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 0.246 
• R-Value Work: 0.205 
• R-Value Observed: 0.209 

Literature

Overcoming antibiotic resistance inPseudomonas aeruginosabiofilms using glycopeptide dendrimers.

Michaud, G., Visini, R., Bergmann, M., Salerno, G., Bosco, R., Gillon, E., Richichi, B., Nativi, C., Imberty, A., Stocker, A., Darbre, T., Reymond, J.L.

(2016) Chem Sci 7: 166-182

• PubMed: 29896342 
• DOI: 10.1039/c5sc03635f
• Primary Citation of Related Structures:  
  5D2A


• PubMed Abstract: 
  

Antibiotic resistance in the opportunistic pathogen Pseudomonas aeruginosa is partly caused by biofilms forming a physical barrier to antibiotic penetration. Here we focused on modifying tetravalent glycopeptide dendrimer ligands of P. aeruginosa lectins LecB or LecA to increase their biofilm inhibition activity. First heteroglycoclusters were investigated displaying one pair each of LecB specific fucosyl groups and LecA specific galactosyl groups and binding simultaneously to both lectins, one of which gave the first fully resolved crystal structure of a peptide dendrimer as LecB complex providing a structural model for dendrimer-lectin interactions (PDB ; 5D2A). Biofilm inhibition was increased by introducing additional cationic residues in these dendrimers but resulted in bactericidal effects similar to those of non-glycosylated polycationic antimicrobial peptide dendrimers. In a second approach dendrimers displaying four copies of the natural LecB ligand Lewis ^a were prepared leading to slightly stronger LecB binding and biofilm inhibition. Finally synergistic application of a LecB specific non-bactericidal antibiofilm dendrimer with the antibiotic tobramycin at sub-inhibitory concentrations of both compounds allowed effective biofilm inhibition and dispersal.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucose-binding lectin	A, B	114	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: lecB, ERS445055_01627, PA8380_17510, PAE221_03716, PAMH19_1713, YQ19_10010
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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ZDC-ALA-PRO-ALA-LYS-PHE-CYS-ALA-PRO-ALA-PHB-GAL	C	6	synthetic construct	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ZDC-ALA-PRO-ALA-LYS-PHE-CYS-ALA-PRO-ALA-PHB-GAL	D, E	3	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZDC	L [auth D], M [auth E]	3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid C8 H14 O6 YTZUDUWVQZSKNN-OASCRQMUSA-N
GAL	K [auth C]	beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
PHB	J [auth C]	P-HYDROXYBENZOIC ACID C7 H6 O3 FJKROLUGYXJWQN-UHFFFAOYSA-N
CA	F [auth A], G [auth A], H [auth B], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 0.246 
• R-Value Work: 0.205 
• R-Value Observed: 0.209 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.107	α = 90
b = 105.107	β = 90
c = 111.092	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-08-05 
• Released Date: 2016-02-10 
Deposition Author(s): Michaud, G., Visini, R., Stocker, A., Darbre, T., Reymond, J.L.

Revision History  

• Version 1.0: 2016-02-10
  Type: Initial release
  
• Version 1.1: 2018-07-11
  Changes: Data collection, Database references
• Version 1.2: 2019-05-08
  Changes: Advisory, Data collection, Derived calculations
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary