PDB-9i80: LecA in complex with a tolcapone derivative glycomimetic

ID or keywords:

Entry

Database: PDB / ID: 9i80

Title

LecA in complex with a tolcapone derivative glycomimetic

Components

PA-I galactophilic lectin

Keywords

SUGAR BINDING PROTEIN / drug repurposing / glycomimetics / catechols / lectins / inhibitors

Function / homology

Function and homology information

heterophilic cell-cell adhesion / carbohydrate binding / periplasmic space / cell surface / cytoplasm
Similarity search - Function

Biological species

Pseudomonas aeruginosa PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Varrot, A.

Funding support

France,

Germany, 2items

Citation

Journal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: The Parkinson's Disease Drug Tolcapone and Analogues are Potent Glycomimetic Lectin Inhibitors of Pseudomonas aeruginosa LecA.
Authors: Leusmann, S. / Siebs, E. / Kuhaudomlarp, S. / Varrot, A. / Imberty, A. / Kuhn, B. / Lerner, C. / Grether, U. / Titz, A.

History

Deposition	Feb 3, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 22, 2025	Provider: repository / Type: Initial release
Revision 1.1	Nov 12, 2025	Group: Database references / Category: citation / citation_author Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9i80.cif.gz	499.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	9i80_validation.pdf.gz	6.1 MB	Display	wwPDB validaton report
Full document	9i80_full_validation.pdf.gz	6.1 MB	Display
Data in XML	9i80_validation.xml.gz	54 KB	Display
Data in CIF	9i80_validation.cif.gz	72.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i8/9i80 ftp://data.pdbj.org/pub/pdb/validation_reports/i8/9i80	HTTPS FTP

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Related structure data

Related structure data	9i7zC 8guv C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.5281/zenodo.14844040 / Data set type: diffraction image data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: PA-I galactophilic lectin

B: PA-I galactophilic lectin

C: PA-I galactophilic lectin

D: PA-I galactophilic lectin

E: PA-I galactophilic lectin

F: PA-I galactophilic lectin

G: PA-I galactophilic lectin

H: PA-I galactophilic lectin

hetero molecules

105 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: PA-I galactophilic lectin

B: PA-I galactophilic lectin

C: PA-I galactophilic lectin

D: PA-I galactophilic lectin

hetero molecules

defined by author
52.7 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: PA-I galactophilic lectin

F: PA-I galactophilic lectin

G: PA-I galactophilic lectin

H: PA-I galactophilic lectin

hetero molecules

defined by author
52.7 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	81.214, 81.214, 165.029
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	76
Space group name H-M	P4₁

#1: Protein	PA-I galactophilic lectin / PA-IL / Galactose-binding lectin Mass: 12770.137 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: N terminal methionine cleaved / Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: lecA, pa1L, PA2570 / Plasmid: LecA-Pet25b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05097
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-A1I1G / pentyl 3-[3-nitro-4,5-bis(oxidanyl)phenyl]carbonylbenzoate Mass: 373.357 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₉H₁₉NO₇ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 893 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.5 Å³/Da / Density % sol: 50.81 % / Description: cube
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 26% Peg 6K, 1M LiCl and 100 mM sodium acetate pH 4.5

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SOLEIL

/ Beamline: PROXIMA 1 / Wavelength: 0.9786 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2023

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9786 Å / Relative weight: 1

Reflection twin

Type	Crystal-ID	ID	Operator	Domain-ID	Fraction
pseudo-merohedral	1	1	H, K, L	1	0.8671
pseudo-merohedral	2	2	-K, -H, -L	2	0.1329

Reflection

Resolution: 1.95→47.13 Å / Num. obs: 77579 / % possible obs: 100 % / Redundancy: 7.7 % / B_iso Wilson estimate: 27.95 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.126 / R_pim(I) all: 0.074 / R_rim(I) all: 0.146 / Net I/av σ(I): 4 / Net I/σ(I): 8.7

Reflection shell

Resolution: 1.95→1.99 Å / R_merge(I) obs: 0.723 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4594 / CC_1/2: 0.798 / R_pim(I) all: 0.442 / R_rim(I) all: 0.852 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
Aimless	0.7.15	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.95→47.13 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.951 / SU B: 4.838 / SU ML: 0.082 / Cross valid method: FREE R-VALUE / ESU R: 0.032 / ESU R Free: 0.029
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2025	3915	5.05 %
R_work	0.1661	73603	-
all	0.168	-	-
obs	-	77518	99.977 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 27.369 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-8.471 Å²	-0 Å²	-0 Å²
2-	-	-8.471 Å²	-0 Å²
3-	-	-	16.943 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→47.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7196	0	215	893	8304

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.012	7662
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	6882
X-RAY DIFFRACTION	r_angle_refined_deg	1.925	1.755	10491
X-RAY DIFFRACTION	r_angle_other_deg	0.692	1.732	15803
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.542	5	974
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	24.948	14.836	61
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.519	10	1045
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.159	10	327
X-RAY DIFFRACTION	r_chiral_restr	0.109	0.2	1097
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.02	9452
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1788
X-RAY DIFFRACTION	r_nbd_refined	0.205	0.2	1446
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.212	0.2	6393
X-RAY DIFFRACTION	r_nbtor_refined	0.189	0.2	3887
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.092	0.2	4003
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.157	0.2	654
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.017	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined	0.119	0.2	34
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.146	0.2	26
X-RAY DIFFRACTION	r_nbd_other	0.177	0.2	96
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.143	0.2	13
X-RAY DIFFRACTION	r_mcbond_it	2.852	2.119	3899
X-RAY DIFFRACTION	r_mcbond_other	2.852	2.119	3899
X-RAY DIFFRACTION	r_mcangle_it	3.424	3.78	4872
X-RAY DIFFRACTION	r_mcangle_other	3.424	3.78	4873
X-RAY DIFFRACTION	r_scbond_it	3.648	2.42	3763
X-RAY DIFFRACTION	r_scbond_other	3.648	2.42	3764
X-RAY DIFFRACTION	r_scangle_it	4.843	4.311	5619
X-RAY DIFFRACTION	r_scangle_other	4.843	4.311	5620
X-RAY DIFFRACTION	r_lrange_it	6.084	24.314	8973
X-RAY DIFFRACTION	r_lrange_other	6.023	23.554	8799

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.95-2.001	0.336	275	0.283	5415	X-RAY DIFFRACTION	99.8421
2.001-2.055	0.271	336	0.243	5215	X-RAY DIFFRACTION	99.946
2.055-2.115	0.299	253	0.216	5205	X-RAY DIFFRACTION	99.9817
2.115-2.18	0.261	226	0.191	5016	X-RAY DIFFRACTION	100
2.18-2.251	0.236	250	0.186	4864	X-RAY DIFFRACTION	100
2.251-2.33	0.228	255	0.177	4676	X-RAY DIFFRACTION	100
2.33-2.418	0.227	216	0.172	4550	X-RAY DIFFRACTION	100
2.418-2.516	0.196	238	0.16	4338	X-RAY DIFFRACTION	100
2.516-2.628	0.224	211	0.164	4207	X-RAY DIFFRACTION	100
2.628-2.755	0.235	205	0.169	4000	X-RAY DIFFRACTION	100
2.755-2.904	0.213	224	0.17	3759	X-RAY DIFFRACTION	99.9749
2.904-3.079	0.201	180	0.168	3615	X-RAY DIFFRACTION	100
3.079-3.291	0.21	195	0.17	3384	X-RAY DIFFRACTION	100
3.291-3.553	0.181	164	0.163	3141	X-RAY DIFFRACTION	100
3.553-3.89	0.165	177	0.152	2878	X-RAY DIFFRACTION	100
3.89-4.345	0.153	142	0.134	2614	X-RAY DIFFRACTION	100
4.345-5.011	0.152	121	0.126	2352	X-RAY DIFFRACTION	100
5.011-6.119	0.175	102	0.137	1978	X-RAY DIFFRACTION	100
6.119-8.582	0.188	91	0.153	1516	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.5742	-0.2475	0.0099	0.5753	0.4188	0.3964	-0.0665	-0.0198	0.01	-0.0003	0.077	0.0046	-0.002	0.0681	-0.0104	0.0598	0.0087	-0.0042	0.13	-0.0203	0.0611	33.5014	-5.611	-11.2484
2	1.0159	0.2955	0.073	0.2301	0.0321	0.2134	-0.057	-0.0544	0.0388	0.0087	0.0392	0.0315	-0.0156	0.034	0.0178	0.0327	0.0164	-0.0013	0.1407	-0.0426	0.057	34.2294	9.227	5.1454
3	0.7742	0.0733	-0.0452	0.1539	0.242	0.4302	-0.0273	0.0175	0.0219	0.027	0.016	0.0196	0.0241	0.018	0.0113	0.0578	0.0021	0.0248	0.1163	-0.0105	0.069	-6.1249	7.933	8.1966
4	1.1659	-0.3231	-0.2076	0.269	0.2683	0.2884	-0.0385	0.1095	-0.0588	0.0105	-0.0221	0.0435	0.0079	-0.0217	0.0606	0.0288	-0.0168	0.0111	0.1376	-0.036	0.0718	-6.7637	-2.2896	-11.4599
5	0.8239	-0.049	0.2639	0.4634	0.3388	0.3626	-0.0314	-0.0259	0.0068	0.0036	0.0612	-0.0183	0.0037	0.0411	-0.0298	0.0336	0.011	-0.0088	0.1354	-0.0378	0.0814	73.1307	34.2025	-12.5371
6	1.4788	0.2773	0.2106	0.1757	0.2817	0.5065	-0.0763	-0.0233	0.0231	-0.0069	0.0155	0.0277	0.0002	0.0237	0.0608	0.0121	0.0072	-0.017	0.143	-0.0507	0.0749	74.0989	48.087	4.6802
7	0.7645	0.0618	-0.1887	0.241	0.4296	0.9205	-0.0076	0.0247	0.02	0.0274	0.0496	-0.0209	0.0473	-0.0072	-0.042	0.0076	0.0246	0.0045	0.1856	-0.0125	0.0502	33.7669	46.885	7.683
8	0.7549	-0.1238	0.1683	0.426	0.2152	0.1835	-0.0514	0.0319	-0.027	-0.0349	0.034	0.0378	-0.0364	0.0353	0.0173	0.0146	-0.0187	-0.0016	0.176	-0.0094	0.0531	32.8983	37.3858	-12.2536
9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.0934	0	0	0.0934	0	0.0934	0	0	0

Refinement TLS group

Selection: ALL

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