2JDH

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


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 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


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

  • 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 ...

    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.


    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

    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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FUCOSE-BINDING LECTIN PA-IILA, B, C, D115Pseudomonas aeruginosaMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HYN5
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE, F, G 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G35446HX
GlyCosmos:  G35446HX
GlyGen:  G35446HX
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC

Download Ideal Coordinates CCD File 
H [auth A]alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
TA5
Query on TA5

Download Ideal Coordinates CCD File 
K [auth B],
Q [auth C],
R [auth D]
2H-1,2,3-TRIAZOL-4-YLMETHANOL
C3 H5 N3 O
OADYBXHYXPEGHX-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
N [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
L [auth B],
M [auth B],
O [auth C],
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
 Ligand Interaction
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 = 52.552α = 90
b = 72.829β = 94.29
c = 54.359γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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