SMTL ID : 7z62.1

Structure of the LecA lectin from Pseudomonas aeruginosa in complex with a biaryl-thiogalactoside

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.53 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: IEC.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:Y.36, A:D.100, A:T.104 CA.4: 5 residues within 4Å: Chain B: Y.36, D.100, T.104, N.107, N.108 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Y.36, B:D.100, B:T.104, H2O.10 CA.6: 6 residues within 4Å: Chain C: Y.36, D.100, T.104, N.107, N.108 Ligands: IEC.7 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:Y.36, C:D.100, C:T.104 CA.9: 5 residues within 4Å: Chain D: Y.36, D.100, T.104, N.107, N.108 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:Y.36, D:D.100, D:T.104, H2O.25

2 x IEC: (2R,3R,4S,5R,6S)-2-(hydroxymethyl)-6-[4-[1-(4-methoxyphenyl)ethenyl]phenyl]sulfanyl-oxane-3,4,5-triol(Non-covalent)

IEC.2: 15 residues within 4Å: Chain A: Y.36, H.50, P.51, Q.53, D.100, V.101, T.104, N.107 Chain B: Y.36, G.37, P.38, H.50, Q.53, N.107 Ligands: CA.1 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:Y.36, B:P.38, A:P.51 Hydrogen bonds: B:Q.53, A:D.100, A:N.107 Water bridges: A:H.50, A:T.104, A:N.107 IEC.7: 15 residues within 4Å: Chain C: Y.36, H.50, P.51, Q.53, D.100, V.101, T.104, N.107 Chain D: Y.36, G.37, P.38, H.50, Q.53, N.107 Ligands: CA.6 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:P.51, D:Y.36, D:P.38 Hydrogen bonds: C:D.100, C:N.107, D:Q.53 Water bridges: C:H.50, C:T.104, C:N.107

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

EDO.3: 9 residues within 4Å: Chain A: G.43, P.44, Q.45, T.79 Chain C: G.43, P.44, Q.45, T.79 Ligands: EDO.8 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:G.43, C:Q.45, C:Q.45, A:G.43, A:Q.45, A:Q.45 Water bridges: C:G.43, A:G.43 EDO.5: 9 residues within 4Å: Chain B: G.43, P.44, Q.45, T.79 Chain D: G.43, P.44, Q.45, T.79 Ligands: EDO.10 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:G.43, D:G.43, D:Q.45, D:Q.45, B:G.43, B:G.43, B:Q.45, B:Q.45 EDO.8: 9 residues within 4Å: Chain A: G.43, P.44, Q.45, T.79 Chain C: G.43, P.44, Q.45, T.79 Ligands: EDO.3 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:G.43, C:Q.45, C:Q.45, A:G.43, A:Q.45, A:Q.45 Water bridges: C:G.43, A:G.43 EDO.10: 9 residues within 4Å: Chain B: G.43, P.44, Q.45, T.79 Chain D: G.43, P.44, Q.45, T.79 Ligands: EDO.5 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:G.43, D:G.43, D:Q.45, D:Q.45, B:G.43, B:G.43, B:Q.45, B:Q.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bruneau, A. et al., Discovery of potent 1,1-diarylthiogalactoside glycomimetic inhibitors of Pseudomonas aeruginosa LecA with antibiofilm properties. Eur.J.Med.Chem. (2022)

Release Date

2023-01-18

Peptides

PA-I galactophilic lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

C
AAA

D
BBB

PA-I galactophilic lectin

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