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 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 49.44 kDa 
• Atom Count: 4379 
• Modelled Residue Count: 456 
• Deposited Residue Count: 460 
• Unique protein chains: 1

2JDH

Lectin PA-IIL of P.aeruginosa complexed with disaccharide derivative

• PDB DOI: 10.2210/pdb2JDH/pdb

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


• Deposited: 2007-01-09 Released: 2007-07-24 
• Deposition Author(s): Marotte, K., Sabin, C., Preville, C., Pymbock, M., Deguise, I., Wimmerova, M., Mitchell, E.P., Imberty, A., Roy, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.131 
• R-Value Work: 0.107 
• R-Value Observed: 0.108 

Literature

X-Ray Structures and Thermodynamics of the Interaction of Pa-Iil from Pseudomonas Aeruginosa with Disaccharide Derivatives.

Marotte, K., Sabin, C., Preville, C., Pymbock, M., Wimmerova, M., Mitchell, E.P., Imberty, A., Roy, R.

(2007) ChemMedChem 2: 1328

• PubMed: 17623286 
• DOI: 10.1002/cmdc.200700100
• Primary Citation of Related Structures:  
  2JDH, 2JDK


• PubMed Abstract: 
  

Pseudomonas aeruginosa is an opportunistic bacterium showing increasing resistance to antibiotics and consequently represents elevated threatening problems in hospital environments, particularly for cystic fibrosis patients. The use of glycomimetics as an anti-adhesive strategy against microorganisms may complement the use of antibiotics. PA-IIL lectin (LecB) from P. aeruginosa constitutes an appealing target for antibacterial agents, as it has been proposed to play a key role in binding to airway epithelia and/or to be involved in biofilm formation. The lectin has an unusually high affinity for L-fucose and related oligosaccharides. In the work presented herein, the disaccharide alphaFuc1-4GlcNAc is used as a scaffold toward the synthesis of a series of glycomimetic derivatives. Microcalorimetry and structural studies indicate that several of the derivatives are potent inhibitors of the lectin, with affinity in the same range as the best known natural ligand, Lewis a, and could represent interesting leads for the development of future antibacterial compounds.

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Related Citations: 

• Structural Basis for Oligosaccharide-Mediated Adhesion of Pseudomonas Aeruginosa in the Lungs of Cystic Fibrosis Patients
  Mitchell, E., Houles, C., Sudakevitz, D., Wimmerova, M., Gautier, C., Perez, S., Wu, A., Gilboa-Garber, N., Imberty, A.
  (2002) Nat Struct Biol 9: 918

• Structural Basis for the Interaction between Human Milk Oligosaccharides and the Bacterial Lectin Pa-Iil of Pseudomonas Aeruginosa.
  Perret, S., Sabin, C., Dumon, C., Pokorna, M., Gautier, C., Galanina, O., Ilia, S., Bovin, N., Nicaise, M., Desmadril, M., Gilboa-Garber, N., Wimmerova, M., Mitchell, E., Imberty, A.
  (2005) Biochem J 389: 325

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Organizational Affiliation: 

Equipe PharmaQAM, Département de Chimie et de Biochimie, Université du Québec à Montréal, 8888, Succ. Centre-Ville, Montréal (Québec) H3C 3P8, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FUCOSE-BINDING LECTIN PA-IIL	A, B, C, D	115	Pseudomonas aeruginosa	Mutation(s): 0
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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-L-fucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G	2		N/A
Glycosylation Resources
GlyTouCan:  G35446HX GlyCosmos:  G35446HX GlyGen:  G35446HX

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FUC	H [auth A]	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
TA5	K [auth B], Q [auth C], R [auth D]	2H-1,2,3-TRIAZOL-4-YLMETHANOL C3 H5 N3 O OADYBXHYXPEGHX-UHFFFAOYSA-N
SO4	N [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	I [auth A], J [auth A], L [auth B], M [auth B], O [auth C], P [auth C], S [auth D], T [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.131 
• R-Value Work: 0.107 
• R-Value Observed: 0.108 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.552	α = 90
b = 72.829	β = 94.29
c = 54.359	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-01-09 
• Released Date: 2007-07-24 
Deposition Author(s): Marotte, K., Sabin, C., Preville, C., Pymbock, M., Deguise, I., Wimmerova, M., Mitchell, E.P., Imberty, A., Roy, R.

Revision History  

• Version 1.0: 2007-07-24
  Type: Initial release
  
• Version 1.1: 2014-02-19
  Changes: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary