2BOJ

crystal Structure of pseudomonas aeruginosa lectin (PA-IIL) complexed with methyl-B-D-Arabinopyranoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Binding of Different Monosaccharides by Lectin Pa-Iil from Pseudoman Aeruginosa: Thermodynamics Data Correlated with X-Ray Structures.

Sabin, C.D.Mitchell, E.P.Pokarna, M.Gautier, C.Utille, J.-P.Wimmerova, M.Imberty, A.

(2006) FEBS Lett 580: 982

  • DOI: 10.1016/j.febslet.2006.01.030
  • Primary Citation of Related Structures:  
    2BP6, 2BOJ

  • PubMed Abstract: 
  • The lectin from Pseudomonas aeruginosa (PA-IIL) is involved in host recognition and biofilm formation. Lectin not only displays an unusually high affinity for fucose but also binds to L-fucose, L-galactose and D-arabinose that differ only by the grou ...

    The lectin from Pseudomonas aeruginosa (PA-IIL) is involved in host recognition and biofilm formation. Lectin not only displays an unusually high affinity for fucose but also binds to L-fucose, L-galactose and D-arabinose that differ only by the group at position 5 of the sugar ring. Isothermal calorimetry experiments provided precise determination of affinity for the three methyl-glycosides and revealed a large enthalpy contribution. The crystal structures of the complexes of PA-IIL with L-galactose and Met-beta-D-arabinoside have been determined and compared with the PA-IIL/fucose complex described previously. A combination of the structures and thermodynamics provided clues for the role of the hydrophobic group in affinity.


    Related Citations: 
    • High Affinity Fucose Binding of Pseudomonas Aeruginosa Lectin Pa-Iil: 1.0 A Resolution Crystal Structure of the Complex Combined with Thermodynamics and Computational Chemistry Approaches
      Mitchell, E., Sabin, C.D., Snajdrova, L., Pokorna, M., Perret, S., Gautier, C., Hofr, C., Gilboa-Garber, N., Koca, J., Wimmerova, M., Imberty, A.
      (2005) Proteins 58: 735

    Organizational Affiliation

    CERMAV-CNRS (affiliated with Université Joseph Fourier), 601 rue de la Chimie, Grenoble BP53, F-38041 Grenoble cedex 09, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PSEUDOMONAS AERUGINOSA LECTIN IIABCD114Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: lecBPA3361
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ARW
Query on ARW

Download CCD File 
A, B, C, D
methyl beta-D-arabinopyranoside
C6 H12 O5
ZBDGHWFPLXXWRD-ARQDHWQXSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ARWKd:  1700   nM  Binding MOAD
ARWKd :  1700   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.636α = 90
b = 80.168β = 109.92
c = 52.517γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-22
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary