4CP9

Crystal structure OF lecA lectin complexed with a divalent galactoside at 1.65 angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A Leca Ligand Identified from a Galactoside-Conjugate Array Inhibits Host Cell Invasion by Pseudomonas Aeruginosa.

Novoa, A.Eierhoff, T.Topin, J.Varrot, A.Barluenga, S.Imberty, A.Romer, W.Winssinger, N.

(2014) Angew Chem Int Ed Engl 53: 8885

  • DOI: 10.1002/anie.201402831
  • Primary Citation of Related Structures:  
    4CP9, 4CPB

  • PubMed Abstract: 
  • Lectin LecA is a virulence factor of Pseudomonas aeruginosa involved in lung injury, mortality, and cellular invasion. Ligands competing with human glycoconjugates for LecA binding are thus promising candidates to counteract P. aeruginosa infections. ...

    Lectin LecA is a virulence factor of Pseudomonas aeruginosa involved in lung injury, mortality, and cellular invasion. Ligands competing with human glycoconjugates for LecA binding are thus promising candidates to counteract P. aeruginosa infections. We have identified a novel divalent ligand from a focused galactoside(Gal)-conjugate array which binds to LecA with very high affinity (Kd = 82 nM). Crystal structures of LecA complexed with the ligand together with modeling studies confirmed its ability to chelate two binding sites of LecA. The ligand lowers cellular invasiveness of P. aeruginosa up to 90 % when applied in the range of 0.05-5 μM. Hence, this ligand might lead to the development of drugs against P. aeruginosa infection.


    Organizational Affiliation

    Department of Organic Chemistry, University of Geneva (Switzerland).



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PA-I GALACTOPHILIC LECTINA121Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: lecApa1LPA2570
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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PA-I GALACTOPHILIC LECTINBCD121Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: lecApa1LPA2570
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CN8
Query on CN8

Download Ideal Coordinates CCD File 
A, B, C, D
(4S)-N-ethyl-4-{[N-methyl-3-(1-{2-[(4-sulfanylbenzoyl)amino]ethyl}-1H-1,2,3-triazol-4-yl)-L-alanyl]amino}-L-prolinamide
C22 H32 N8 O3 S
VTNMGGUGQYETGZ-SNRMKQJTSA-N
 Ligand Interaction
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
A, B, C, D
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
GAL
Query on GAL

Download Ideal Coordinates CCD File 
A, B, C, D
beta-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS
AL-PEPTIDE LINKINGC3 H7 N O5 SCYS
TRO
Query on TRO
AL-PEPTIDE LINKINGC11 H12 N2 O3TRP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.876α = 90
b = 66.259β = 90
c = 159.427γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2015-04-22
    Changes: Derived calculations, Non-polymer description, Other
  • Version 1.2: 2016-12-28
    Changes: Structure summary
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary