Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A4B3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 7-mer - A4B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 108.72 kDa 
• Atom Count: 8681 
• Modelled Residue Count: 991 
• Deposited Residue Count: 1000 
• Unique protein chains: 2

4LKD

Crystal Structure of Pseudomonas aeruginosa Lectin LecA Complexed with GalA-QRS at 2.31 A Resolution

• DOI: 10.2210/pdb4LKD/pdb

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


• Deposited: 2013-07-07 Released: 2013-12-18 
• Deposition Author(s): Kadam, R.U., Stocker, A., Reymond, J.-L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 0.247 
• R-Value Work: 0.215 
• R-Value Observed: 0.216 

Literature

Structure-Based Optimization of the Terminal Tripeptide in Glycopeptide Dendrimer Inhibitors of Pseudomonas aeruginosa Biofilms Targeting LecA.

Kadam, R.U., Bergmann, M., Garg, D., Gabrieli, G., Stocker, A., Darbre, T., Reymond, J.-L.

(2013) Chemistry 19: 17054-17063

• PubMed: 24307364 
• DOI: 10.1002/chem.201302587
• Primary Citation of Related Structures:  
  4LKD, 4LKE, 4LKF


• PubMed Abstract: 
  

The galactopeptide dendrimer GalAG2 ((β-Gal-OC6H4CO-Lys-Pro-Leu)4(Lys-Phe-Lys-Ile)2Lys-His-Ile-NH2) binds strongly to the Pseudomonas aeruginosa (PA) lectin LecA, and it inhibits PA biofilms, as well as disperses already established ones. By starting with the crystal structure of the terminal tripeptide moiety GalA-KPL in complex with LecA, a computational mutagenesis study was carried out on the galactotripeptide to optimize the peptide-lectin interactions. 25 mutants were experimentally evaluated by a hemagglutination inhibition assay, 17 by isothermal titration calorimetry, and 3 by X-ray crystallography. Two of these tripeptides, GalA-KPY (dissociation constant (K(D))=2.7 μM) and GalA-KRL (K(D)=2.7 μM), are among the most potent monovalent LecA ligands reported to date. Dendrimers based on these tripeptide ligands showed improved PA biofilm inhibition and dispersal compared to those of GalAG2, particularly G2KPY ((β-Gal-OC6H4CO-Lys-Pro-Tyr)4(Lys-Phe-Lys-Ile)2Lys-His-Ile-NH2). The possibility to retain and even improve the biofilm inhibition in several analogues of GalAG2 suggests that it should be possible to fine-tune this dendrimer towards therapeutic use by adjusting the pharmacokinetic parameters in addition to the biofilm inhibition through amino acid substitutions.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne (Switzerland), Fax: [phone].

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  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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide QRSA	I, J, K, L, M, N, O, P	4	N/A	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GAL (Subject of Investigation/LOI)	AA [auth F], CA [auth G], EA [auth H], Q [auth A], S [auth B], U [auth C], W [auth D], Y [auth E]	beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
PHB	GA [auth I], HA [auth J], IA [auth K], JA [auth L], KA [auth M], LA [auth N], MA [auth O], NA [auth P]	P-HYDROXYBENZOIC ACID C7 H6 O3 FJKROLUGYXJWQN-UHFFFAOYSA-N
CA	BA [auth F], DA [auth G], FA [auth H], R [auth A], T [auth B], V [auth C], X [auth D], Z [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 0.247 
• R-Value Work: 0.215 
• R-Value Observed: 0.216 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.216	α = 90
b = 149.239	β = 110.96
c = 87.018	γ = 90

Software Package:

Software Name	Purpose
SLSPSI	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2013-07-07 
• Released Date: 2013-12-18 
Deposition Author(s): Kadam, R.U., Stocker, A., Reymond, J.-L.

Revision History  

• Version 1.0: 2013-12-18
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary