Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 50.07 kDa 
• Atom Count: 4049 
• Modelled Residue Count: 456 
• Deposited Residue Count: 456 
• Unique protein chains: 1

6R35

Structure of the LecB lectin from Pseudomonas aeruginosa strain PAO1 in complex with lewis x tetrasaccharide

• PDB DOI: 10.2210/pdb6R35/pdb

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


• Deposited: 2019-03-19 Released: 2019-06-12 
• Deposition Author(s): Lepsik, M., Sommer, R., Kuhaudomlarp, S., Lelimousin, M., Varrot, A., Titz, A., Imberty, A.
• Funding Organization(s): European Union

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.176 
• R-Value Work: 0.132 
• R-Value Observed: 0.134 

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
• Primary Citation of Related Structures:  
  5A70, 6R35


• 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	Image
Fucose-binding lectin PA-IIL	B [auth A], C [auth B], D [auth C], A [auth D]	114	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: lecB, PA3361
UniProt
Find proteins for Q9HYN5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HYN5  Go to UniProtKB:  Q9HYN5

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H	3		N/A
Glycosylation Resources
GlyTouCan:  G00051MO GlyCosmos:  G00051MO GlyGen:  G00051MO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	K [auth D], W [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	L [auth D], P [auth A], Q [auth A], T [auth B], U [auth B], X [auth C], Y [auth C], Z [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	I [auth D], J [auth D], M [auth D], N [auth A], O [auth A], R [auth A], S [auth B], V [auth C]	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_900119	E, F, G, H	Lewis X antigen, beta anomer	Oligosaccharide / Antigen		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.176 
• R-Value Work: 0.132 
• R-Value Observed: 0.134 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.603	α = 90
b = 72.481	β = 114.62
c = 62.061	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-03-19 
• Released Date: 2019-06-12 
Deposition Author(s): Lepsik, M., Sommer, R., Kuhaudomlarp, S., Lelimousin, M., Varrot, A., Titz, A., Imberty, A.

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Funding Organization	Location	Grant Number
European Union	France	795605

Revision History  

• Version 1.0: 2019-06-12
  Type: Initial release
  
• Version 1.1: 2019-09-18
  Changes: Data collection, Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary