SMTL ID : 9i7z.1

LecA in complex with 2-fluoro non-carbohydrate glycomimetic

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: Y.36, D.100, T.104, N.107, N.108 Ligands: 01.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:Y.36, A:D.100, A:T.104 CA.7: 6 residues within 4Å: Chain B: Y.36, D.100, T.104, N.107, N.108 Ligands: 01.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:Y.36, B:D.100, B:T.104 CA.10: 6 residues within 4Å: Chain C: Y.36, D.100, T.104, N.107, N.108 Ligands: 01.11 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:Y.36, C:D.100, C:T.104 CA.16: 6 residues within 4Å: Chain D: Y.36, D.100, T.104, N.107, N.108 Ligands: 01.17 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:Y.36, D:D.100, D:T.104

4 x 01: [2,6-bis(fluoranyl)phenyl]-[3-nitro-4,5-bis(oxidanyl)phenyl]methanone

01.2: 8 residues within 4Å: Chain A: Y.36, H.50, Q.53, D.100, V.101, T.104, N.107 Ligands: CA.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Q.53, A:Q.53, A:V.101 Hydrogen bonds: A:Y.36, A:T.104, A:N.107 Water bridges: A:Q.53 01.8: 8 residues within 4Å: Chain B: Y.36, H.50, Q.53, D.100, V.101, T.104, N.107 Ligands: CA.7 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Q.53 Hydrogen bonds: B:Y.36, B:D.100, B:T.104, B:N.107 01.11: 9 residues within 4Å: Chain C: Y.36, H.50, Q.53, D.100, V.101, T.104, N.107 Ligands: CA.10, ACT.13 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Q.53 Hydrogen bonds: C:Y.36, C:T.104, C:N.107 Water bridges: C:Q.53 01.17: 8 residues within 4Å: Chain D: Y.36, H.50, Q.53, D.100, V.101, T.104, N.107 Ligands: CA.16 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:Q.53 Hydrogen bonds: D:Y.36, D:D.100, D:T.104, D:N.107 Water bridges: D:Q.53

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.3: 10 residues within 4Å: Chain A: E.11, A.12, I.56, K.68, G.70, N.71, S.72, T.95, I.97 Ligands: EDO.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.68, A:N.71, A:N.71

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 1 residues within 4Å: Ligands: 1PE.3 No protein-ligand interaction detected (PLIP)

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 4 residues within 4Å: Chain A: S.17, I.18, I.19, K.118 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: G.43, P.44, Q.45 Chain B: G.43 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain C: G.43, P.44, Q.45 Chain D: G.43 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain C: R.48 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain D: V.6, L.7, N.10, G.13, Q.14 Ligand excluded by PLIP

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.9: 5 residues within 4Å: Chain B: E.11, A.12, I.56, K.68, N.71 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.68, B:N.71 PG4.18: 4 residues within 4Å: Chain D: E.11, A.12, K.68, I.97 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.68

1 x 9YU: 2-[2-[2-[2-[2-[2-(2-methoxyethoxy)ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethanol(Non-covalent)

9YU.12: 6 residues within 4Å: Chain C: A.12, I.56, K.68, G.70, G.73, T.74 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.68 Water bridges: C:T.74, C:T.74

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.13: 3 residues within 4Å: Chain C: Y.36, H.50 Ligands: 01.11 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.36 Salt bridges: C:H.50

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.19: 4 residues within 4Å: Chain D: H.50, H.58, A.60, F.61 1 PLIP interactions: 1 interactions with chain D Water bridges: D:D.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leusmann, S. et al., The Parkinson's Disease Drug Tolcapone and Analogues are Potent Glycomimetic Lectin Inhibitors of Pseudomonas aeruginosa LecA. Angew.Chem.Int.Ed.Engl. (2025)

Release Date

2025-10-22

Peptides

PA-I galactophilic lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

PA-I galactophilic lectin

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