4AL9

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

• PDB DOI: https://doi.org/10.2210/pdb4AL9/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-02 Released: 2013-03-20 
• Deposition Author(s): Blanchard, B., Imberty, A., Varrot, A.

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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 

Literature

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

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

(2014) Proteins 82: 1060

• PubMed: 24123124 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 104.56 kDa 
• Atom Count: 8,195 
• Modelled Residue Count: 968 
• Deposited Residue Count: 968 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PA-I GALACTOPHILIC LECTIN	A, B, C, D, E, F, G, H	121	Pseudomonas aeruginosa PAO1	Mutation(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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose	I, J	2		N/A
Glycosylation Resources
GlyTouCan:  G54976AD GlyCosmos:  G54976AD GlyGen:  G54976AD

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLA	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	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	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

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900037	I, J	alpha-melibiose	Oligosaccharide / Metabolism

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 = 50.07	α = 101.13
b = 58.13	β = 92.89
c = 75.94	γ = 100.98

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-20 
Deposition Author(s): Blanchard, B., Imberty, A., Varrot, A.

Revision History  

• 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