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: 49.43 kDa 
• Atom Count: 3743 
• Residue Count: 456 
• Unique protein chains: 1

3DCQ

LECB (PA-LII) in complex with the synthetic ligand 2G0

• DOI: 10.2210/pdb3DCQ/pdb

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


• Deposited: 2008-06-04 Released: 2009-01-13 
• Deposition Author(s): Johansson, E.M., Crusz, S.A., Kolomiets, E., Buts, L., Kadam, R.U., Cacciarini, M., Bartels, K.M., Diggle, S.P., Camara, M., Williams, P., Loris, R., Nativi, C., Rosenau, F., Jaeger, K.E., Darbre, T., Reymond, J.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.211 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 

Literature

Inhibition and dispersion of Pseudomonas aeruginosa biofilms by glycopeptide dendrimers targeting the fucose-specific lectin LecB.

Johansson, E.M., Crusz, S.A., Kolomiets, E., Buts, L., Kadam, R.U., Cacciarini, M., Bartels, K.M., Diggle, S.P., Camara, M., Williams, P., Loris, R., Nativi, C., Rosenau, F., Jaeger, K.E., Darbre, T., Reymond, J.L.

(2008) Chem Biol 15: 1249-1257

• PubMed: 19101469 
• DOI: 10.1016/j.chembiol.2008.10.009
• Primary Citation of Related Structures:  
  3DCQ


• PubMed Abstract: 
  

The human pathogenic bacterium Pseudomonas aeruginosa produces a fucose-specific lectin, LecB, implicated in tissue attachment and the formation of biofilms. To investigate if LecB inhibition disrupts these processes, high-affinity ligands were obtained by screening two 15,536-member combinatorial libraries of multivalent fucosyl-peptide dendrimers. The most potent LecB-ligands identified were dendrimers FD2 (C-Fuc-LysProLeu)(4)(LysPheLysIle)(2)LysHisIleNH(2) (IC(50) = 0.14 microM by ELLA) and PA8 (OFuc-LysAlaAsp)(4)(LysSerGlyAla)(2)LysHisIleNH(2) (IC(50) = 0.11 microM by ELLA). Dendrimer FD2 led to complete inhibition of P. aeruginosa biofilm formation (IC(50) approximately 10 microM) and induced complete dispersion of established biofilms in the wild-type strain and in several clinical P. aeruginosa isolates. These experiments suggest that LecB inhibition by high-affinity multivalent ligands could represent a therapeutic approach against P. aeruginosa infections by inhibition of biofilm formation and dispersion of established biofilms.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH-3012 Berne, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucose-binding lectin PA-IIL	A, B, C, D	114	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: lecB, PA3361
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2G0	A, B, C, D	(2S)-1-[(2S)-6-amino-2-({[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyltetrahydro-2H-pyran-2-yl]acetyl}amino)hexanoyl]-N-[(1S)-1-carbamoyl-3-methylbutyl]pyrrolidine-2-carboxamide C25 H45 N5 O8 GOIFOXKHMWJIPQ-OXQNIBOTSA-N
CA	A, B, C, D	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
2G0	IC50 :  5940   nM  PDBBind
2G0	IC50:  5940   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.211 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.32	α = 90
b = 75.52	β = 90
c = 99.03	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-06-04 
• Released Date: 2009-01-13 
Deposition Author(s): Johansson, E.M., Crusz, S.A., Kolomiets, E., Buts, L., Kadam, R.U., Cacciarini, M., Bartels, K.M., Diggle, S.P., Camara, M., Williams, P., Loris, R., Nativi, C., Rosenau, F., Jaeger, K.E., Darbre, T., Reymond, J.L.

Revision History 

• Version 1.0: 2009-01-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description