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 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 49.61 kDa 
• Atom Count: 4025 
• Residue Count: 456 
• Unique protein chains: 1

3ZDV

Crystal structure of the LecB lectin from Pseudomonas aeruginosa in complex with Methyl 6-(2,4,6-trimethylphenylsulfonylamido)-6-deoxy-alpha-D-mannopyranoside

• DOI: 10.2210/pdb3ZDV/pdb

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


• Deposited: 2012-11-30 Released: 2013-09-18 
• Deposition Author(s): Hauck, D., Joachim, I., Frommeyer, B., Varrot, A., Philipp, B., MOller, H.M., Imberty, A., Exner, T.E., Titz, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.145 
• R-Value Work: 0.115 
• R-Value Observed: 0.116 

Literature

Discovery of Two Classes of Potent Glycomimetic Inhibitors of Pseudomonas Aeruginosa Lecb with Distinct Binding Modes.

Hauck, D., Joachim, I., Frommeyer, B., Varrot, A., Philipp, B., Moller, H.M., Imberty, A., Exner, T.E., Titz, A.

(2013) ACS Chem Biol 8: 1775

• PubMed: 23719508 
• DOI: 10.1021/cb400371r
• Primary Citation of Related Structures:  
  3ZDV


• PubMed Abstract: 
  

The treatment of infections due to the opportunistic pathogen Pseudomonas aeruginosa is often difficult, as a consequence of bacterial biofilm formation. Such a protective environment shields the bacterium from host defense and antibiotic treatment and secures its survival. One crucial factor for maintenance of the biofilm architecture is the carbohydrate-binding lectin LecB. Here, we report the identification of potent mannose-based LecB inhibitors from a screening of four series of mannosides in a novel competitive binding assay for LecB. Cinnamide and sulfonamide derivatives are inhibitors of bacterial adhesion with up to a 20-fold increase in affinity to LecB compared to the natural ligand methyl mannoside. Because many lectins of the host require terminal saccharides (e.g., fucosides), such capped structures as reported here may offer a beneficial selectivity profile for the pathogenic lectin. Both classes of compounds show distinct binding modes at the protein, offering the advantage of a simultaneous development of two new lead structures as anti-pseudomonadal drugs with an anti-virulence mode of action.

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Organizational Affiliation: 

Department of Chemistry, University of Konstanz, D-78457 Konstanz, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FUCOSE-BINDING LECTIN PA-IIL	A, B, C, D	115	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: lecB, PA3361
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

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F1A	A, B, C, D	2,4,6-trimethylbenzenesulfonamide C9 H13 N O2 S YECJUZIGFPJWGQ-UHFFFAOYSA-N
MMA	A, B, C, D	methyl alpha-D-mannopyranoside C7 H14 O6 HOVAGTYPODGVJG-VEIUFWFVSA-N
SO4	D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	B	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	A, B, C, D	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.145 
• R-Value Work: 0.115 
• R-Value Observed: 0.116 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.53	α = 90
b = 76.98	β = 90
c = 99.66	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-11-30 
• Released Date: 2013-09-18 
Deposition Author(s): Hauck, D., Joachim, I., Frommeyer, B., Varrot, A., Philipp, B., MOller, H.M., Imberty, A., Exner, T.E., Titz, A.

Revision History 

• Version 1.0: 2013-09-18
  Type: Initial release
  
• Version 1.1: 2013-11-13
  Changes: Other
• Version 1.2: 2017-09-13
  Changes: Data collection, Structure summary
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary