4AL9

Crystal structure of the lectin PA-IL from Pseudomonas aeruginoas in complex with melibiose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Secondary Sugar Binding Site Identified for Leca Lectin from Pseudomonas Aeruginosa.

Blanchard, B.Imberty, A.Varrot, A.

(2014) Proteins 82: 1060

  • DOI: https://doi.org/10.1002/prot.24430
  • Primary Citation of Related Structures:  
    4AL9

  • PubMed Abstract: 

    The galactose-specific lectin LecA from Pseudomonas aeruginosa is a target for the development of new anti-infectious compounds. Sugar based molecules with anti-adhesive properties present great potential in the fight against bacterial infection and biofilm formation. LecA is specific for oligosaccharides with terminal α-galactoside residues and displays strong affinity for melibiose (αGal1-6Glc) with a Kd of 38.8 µM. The crystal structure of LecA/melibiose complex shows classical calcium-bridged binding of αGal in the primary binding site but also revealed a secondary sugar binding site with glucose bound. This sugar binding site is in close proximity to the galactose binding one, is independent of calcium and mainly involves interactions with a symmetry-related protein. This discovery would help to the design of new potent inhibitors targeting both binding sites.


  • Organizational Affiliation

    CERMAV-CNRS, Université de Grenoble and Member of ICMG, BP 53, 38041 Grenoble Cedex 9, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PA-I GALACTOPHILIC LECTIN
A, B, C, D, E
A, B, C, D, E, F, G, H
121Pseudomonas aeruginosa PAO1Mutation(s): 0 
UniProt
Find proteins for Q05097 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q05097 
Go to UniProtKB:  Q05097
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05097
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose
I, J
2N/A
Glycosylation Resources
GlyTouCan:  G54976AD
GlyCosmos:  G54976AD
GlyGen:  G54976AD
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GLA
Query on GLA

Download Ideal Coordinates CCD File 
AA [auth G]
L [auth A]
O [auth B]
Q [auth C]
S [auth D]
AA [auth G],
L [auth A],
O [auth B],
Q [auth C],
S [auth D],
V [auth E]
alpha-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth H],
M [auth A],
T [auth D],
W [auth F],
Y [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
CA [auth H]
K [auth A]
N [auth B]
P [auth C]
R [auth D]
CA [auth H],
K [auth A],
N [auth B],
P [auth C],
R [auth D],
U [auth E],
X [auth F],
Z [auth G]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
GLA BindingDB:  4AL9 Kd: min: 8.75e+4, max: 8.80e+4 (nM) from 2 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.07α = 101.13
b = 58.13β = 92.89
c = 75.94γ = 100.98
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2013-10-30
    Changes: Database references
  • Version 1.2: 2014-05-28
    Changes: Database references
  • Version 1.3: 2015-09-16
    Changes: Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary