5MIH

Crystal structure of the lectin LecA from Pseudomonas aeruginosa in complex with a phenyl-epoxy-galactopyranoside

PDB DOI: https://doi.org/10.2210/pdb5MIH/pdb

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

Deposited: 2016-11-28 Released: 2017-10-11
Deposition Author(s): Wagner, S., Hauk, D., Hofmann, M., Joachim, I., Sommer, R., Muller, R., Imberty, A., Varrot, A., Titz, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.194
R-Value Work: 0.149
R-Value Observed: 0.151

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Covalent Lectin Inhibition and Application in Bacterial Biofilm Imaging.

Wagner, S., Hauck, D., Hoffmann, M., Sommer, R., Joachim, I., Muller, R., Imberty, A., Varrot, A., Titz, A.

(2017) Angew Chem Int Ed Engl 56: 16559-16564

PubMed: 28960731 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/anie.201709368
Primary Citation of Related Structures:
5MIH

PubMed Abstract:
Biofilm formation by pathogenic bacteria is a hallmark of chronic infections. In many cases, lectins play key roles in establishing biofilms. The pathogen Pseudomonas aeruginosa often exhibiting various drug resistances employs its lectins LecA and LecB as virulence factors and biofilm building blocks. Therefore, inhibition of the function of these proteins is thought to have potential in developing "pathoblockers" preventing biofilm formation and virulence. A covalent lectin inhibitor specific to a carbohydrate binding site is described for the first time. Its application in the LecA-specific in vitro imaging of biofilms formed by P. aeruginosa is also reported.

Organizational Affiliation

Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), 66123, Saarbrücken, Germany.

Macromolecule Content

Total Structure Weight: 52.52 kDa
Atom Count: 4,445
Modelled Residue Count: 484
Deposited Residue Count: 484
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PA-I galactophilic lectin	A, B, C, D	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q05097
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7NU Query on 7NU Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain J [auth C] SDF format, chain M [auth D] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain M [auth D]	F [auth A], H [auth B], J [auth C], M [auth D]	phenyl 6,7-anhydro-D-glycero-beta-D-galacto-heptopyranoside C₁₃ H₁₆ O₆ BGULDTQQEDQGRU-LREJFELKSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain M [auth D]
ETE Query on ETE Download Ideal Coordinates CCD File SDF format, chain K [auth C] MOL2 format, chain K [auth C]	K [auth C]	2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C₉ H₂₀ O₅ ZNYRFEPBTVGZDN-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Interactions & Density Focus chain K [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain L [auth D]	E [auth A], G [auth B], I [auth C], L [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain L [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
7NU	Binding MOAD: 5MIH	IC50: 6.40e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.194
R-Value Work: 0.149
R-Value Observed: 0.151
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.343	α = 90
b = 73.771	β = 93.36
c = 101.454	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-10-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-10-11
Type: Initial release
Version 1.1: 2018-01-03
Changes: Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Derived calculations, Structure summary
Version 1.3: 2024-01-17
Changes: Data collection, Database references, Refinement description, Structure summary