4LK6

Crystal Structure of Pseudomonas aeruginosa Lectin LecA Complexed with Chlorophenol Red-b-D-galactopyranoside at 2.86 A Resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

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Literature

CH-pi "T-Shape" Interaction with Histidine Explains Binding of Aromatic Galactosides to Pseudomonas aeruginosa Lectin LecA

Kadam, R.U., Garg, D., Schwartz, J., Visini, R., Sattler, M., Stocker, A., Darbre, T., Reymond, J.L.

(2013) ACS Chem Biol 8: 1925-1930

  • DOI: 10.1021/cb400303w
  • Primary Citation of Related Structures:  
    4LJH, 4LK6, 4LK7

  • PubMed Abstract: 

    • The galactose specific lectin LecA mediates biofilm formation in the opportunistic pathogen P. aeruginosa . The interaction between LecA and aromatic β-galactoside biofilm inhibitors involves an intermolecular CH-π T-shape interaction between C(ε1)-H of residue His50 in LecA and the aromatic ring of the galactoside aglycone ...

    The galactose specific lectin LecA mediates biofilm formation in the opportunistic pathogen P. aeruginosa . The interaction between LecA and aromatic β-galactoside biofilm inhibitors involves an intermolecular CH-π T-shape interaction between C(ε1)-H of residue His50 in LecA and the aromatic ring of the galactoside aglycone. The generality of this interaction was tested in a diverse family of β-galactosides. LecA binding to aromatic β-galactosides (KD ∼ 8 μM) was consistently stronger than to aliphatic β-galactosides (KD ∼ 36 μM). The CH-π interaction was observed in the X-ray crystal structures of six different LecA complexes, with shorter than the van der Waals distances indicating productive binding. Related XH/cation/π-π interactions involving other residues were identified in complexes of aromatic glycosides with a variety of carbohydrate binding proteins such as concanavalin A. Exploiting such interactions might be generally useful in drug design against these targets.

    Organizational Affiliation: 

    Department of Chemistry and Biochemistry, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PA-I galactophilic lectin
A, B, C, D, E, F, G, H, I, J, K, L
A, B, C, D, E, F, G, H, I, J, K, L
121Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: lecA, pa1L, PA2570
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LRD
Query on LRD
Download Ideal Coordinates CCD File 
CA [auth F],
FA [auth G],
IA [auth H],
LA [auth I],
N [auth A],
CA [auth F],
FA [auth G],
IA [auth H],
LA [auth I],
N [auth A],
OA [auth J],
Q [auth B],
RA [auth K],
T [auth C],
UA [auth L],
W [auth D],
Z [auth E]
2-[(E)-(3-chloro-4-hydroxyphenyl)(3-chloro-4-oxocyclohexa-2,5-dien-1-ylidene)methyl]benzenesulfonic acid
C19 H12 Cl2 O5 S
QXTPRQZMDKBTAI-XDHOZWIPSA-N		 Ligand Interaction
GAL
Query on GAL
Download Ideal Coordinates CCD File 
AA [auth E],
DA [auth F],
GA [auth G],
JA [auth H],
MA [auth I],
AA [auth E],
DA [auth F],
GA [auth G],
JA [auth H],
MA [auth I],
O [auth A],
PA [auth J],
R [auth B],
SA [auth K],
U [auth C],
VA [auth L],
X [auth D]
beta-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
BA [auth F],
EA [auth G],
HA [auth H],
KA [auth I],
M [auth A],
BA [auth F],
EA [auth G],
HA [auth H],
KA [auth I],
M [auth A],
NA [auth J],
P [auth B],
QA [auth K],
S [auth C],
TA [auth L],
V [auth D],
Y [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.068α = 90
b = 150.829β = 90
c = 185.817γ = 90
Software Package:
Software NamePurpose
SLSPSIdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-30
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary