Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50.20 kDa 
• Atom Count: 4179 
• Residue Count: 456 
• Unique protein chains: 1

5A70

Structure of the LecB lectin from Pseudomonas aeruginosa strain PA14 in complex with lewis x tetrasaccharide

• DOI: 10.2210/pdb5A70/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Pseudomonas aeruginosa UCBPP-PA14
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-02 Released: 2016-07-27 
• Deposition Author(s): Sommer, R., Wagner, S., Varrot, A., Khaledi, A., Haussler, S., Imberty, A., Titz, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.171 
• R-Value Work: 0.136 
• R-Value Observed: 0.138 

Literature

Induction of rare conformation of oligosaccharide by binding to calcium-dependent bacterial lectin: X-ray crystallography and modelling study.

Lepsik, M., Sommer, R., Kuhaudomlarp, S., Lelimousin, M., Paci, E., Varrot, A., Titz, A., Imberty, A.

(2019) Eur J Med Chem 177: 212-220

• PubMed: 31146126 
• DOI: 10.1016/j.ejmech.2019.05.049
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Pathogenic micro-organisms utilize protein receptors (lectins) in adhesion to host tissues, a process that in some cases relies on the interaction between lectins and human glycoconjugates. Oligosaccharide epitopes are recognized through their three-dimensional structure and their flexibility is a key issue in specificity. In this paper, we analysed by X-ray crystallography the structures of the LecB lectin from two strains of Pseudomonas aeruginosa in complex with Lewis x oligosaccharide present on cell surfaces of human tissues. An unusual conformation of the glycan was observed in all binding sites with a non-canonical syn orientation of the N-acetyl group of N-acetyl-glucosamine. A PDB-wide search revealed that such an orientation occurs only in 4% of protein/carbohydrate complexes. Theoretical chemistry calculations showed that the observed conformation is unstable in solution but stabilised by the lectin. A reliable description of LecB/Lewis x complex by force field-based methods had proven especially challenging due to the special feature of the binding site, two closely apposed Ca ²⁺ ions which induce strong charge delocalisation. By comparing various force-field parametrisations, we propose a general strategy which will be useful in near future for designing carbohydrate-based ligands (glycodrugs) against other calcium-dependent protein receptors.

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Organizational Affiliation: 

Université Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
LECB	A, B, C, D	114	Pseudomonas aeruginosa UCBPP-PA14	Mutation(s): 0  Gene Names: lecB, PA14_20610
Find proteins for A0A0H2ZE85 (Pseudomonas aeruginosa (strain UCBPP-PA14)) Go to UniProtKB:  A0A0H2ZE85

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B, C, D	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GAL	A, B, C, D	BETA-D-GALACTOSE C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
FUC	A, B, C, D	ALPHA-L-FUCOSE C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
SO4	A, C	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	A, B, C, D	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.171 
• R-Value Work: 0.136 
• R-Value Observed: 0.138 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.898	α = 90
b = 63.228	β = 91.2
c = 63.889	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-07-02 
• Released Date: 2016-07-27 
Deposition Author(s): Sommer, R., Wagner, S., Varrot, A., Khaledi, A., Haussler, S., Imberty, A., Titz, A.

Revision History 

• Version 1.0: 2016-07-27
  Type: Initial release
  
• Version 1.1: 2019-08-07
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2020-01-22
  Changes: Data collection, Other, Structure summary