9I7Z | pdb_00009i7z

LecA in complex with 2-fluoro non-carbohydrate glycomimetic

PDB DOI: https://doi.org/10.2210/pdb9I7Z/pdb

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

Deposited: 2025-02-03 Released: 2025-10-22
Deposition Author(s): Varrot, A.
Funding Organization(s): Agence Nationale de la Recherche (ANR), German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.204 (Depositor), 0.214 (DCC)
R-Value Work:
0.158 (Depositor), 0.168 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

The Parkinson's Disease Drug Tolcapone and Analogues are Potent Glycomimetic Lectin Inhibitors of Pseudomonas aeruginosa LecA

Leusmann, S., Siebs, E., Varrot, A., Kuhaudomlarp, S., Imberty, A., Kuhn, B., Lerner, C., Grether, U., Titz, A.

(2025) Angew Chem Int Ed Engl

Macromolecule Content

Total Structure Weight: 53.79 kDa
Atom Count: 4,161
Modeled Residue Count: 483
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 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9YU Query on 9YU Download Ideal Coordinates CCD File SDF format, chain P [auth C] MOL2 format, chain P [auth C] mmCIF format, chain P [auth C]	P [auth C]	2-[2-[2-[2-[2-[2-(2-methoxyethoxy)ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethanol C₁₅ H₃₂ O₈ AGWKUHGLWHMYTG-UHFFFAOYSA-N		Interactions Focus chain P [auth C] Interactions & Density Focus chain P [auth C]
A1IZM (Subject of Investigation/LOI) Query on A1IZM Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain U [auth D] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain U [auth D] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain U [auth D]	F [auth A], L [auth B], O [auth C], U [auth D]	[2,6-bis(fluoranyl)phenyl]-[3-nitro-4,5-bis(oxidanyl)phenyl]methanone C₁₃ H₇ F₂ N O₅ IGCMBTUXZXDHQQ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain U [auth D] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain U [auth D]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain V [auth D] MOL2 format, chain M [auth B] MOL2 format, chain V [auth D] mmCIF format, chain M [auth B] mmCIF format, chain V [auth D]	M [auth B], V [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain V [auth D] Interactions & Density Focus chain M [auth B] Focus chain V [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain W [auth D] MOL2 format, chain W [auth D] mmCIF format, chain W [auth D]	W [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain W [auth D] Interactions & Density Focus chain W [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain Q [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain Q [auth C]	Q [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain Q [auth C] Interactions & Density Focus chain Q [auth C]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain T [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain T [auth D] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain T [auth D]	E [auth A], K [auth B], N [auth C], T [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain T [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain X [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain X [auth D]	I [auth A], J [auth A], R [auth C], S [auth C], X [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain R [auth C] Focus chain S [auth C] Focus chain X [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain R [auth C] Focus chain S [auth C] Focus chain X [auth D]