SMTL ID : 7z63.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 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: IE3.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:Y.36, A:D.100, A:T.104 CA.3: 6 residues within 4Å: Chain B: Y.36, D.100, T.104, N.107, N.108 Ligands: IE3.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:Y.36, B:D.100, B:T.104 CA.5: 6 residues within 4Å: Chain C: Y.36, D.100, T.104, N.107, N.108 Ligands: IE3.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:Y.36, C:D.100, C:T.104 CA.8: 6 residues within 4Å: Chain D: Y.36, D.100, T.104, N.107, N.108 Ligands: IE3.9 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:Y.36, D:D.100, D:T.104

4 x IE3: [3-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]sulfanyl-4-methoxy-phenyl]-(3,4,5-trimethoxyphenyl)methanone(Non-covalent)

IE3.2: 10 residues within 4Å: Chain A: Y.36, P.38, H.50, P.51, Q.53, D.100, V.101, T.104, N.107 Ligands: CA.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.53, A:D.100, A:T.104, A:N.107 Water bridges: A:H.50, A:P.51 pi-Stacking: A:H.50 IE3.4: 9 residues within 4Å: Chain B: Y.36, P.38, H.50, Q.53, D.100, V.101, T.104, N.107 Ligands: CA.3 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.53, B:D.100, B:T.104, B:T.104, B:N.107 Water bridges: B:P.51, B:Q.53 IE3.6: 10 residues within 4Å: Chain C: Y.36, P.38, H.50, P.51, Q.53, D.100, V.101, T.104, N.107 Ligands: CA.5 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:P.51 Hydrogen bonds: C:Q.53, C:D.100, C:T.104, C:T.104, C:N.107 Water bridges: C:Y.36, C:P.51 IE3.9: 8 residues within 4Å: Chain D: Y.36, H.50, Q.53, D.100, V.101, T.104, N.107 Ligands: CA.8 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.100, D:T.104, D:T.104, D:N.107 Water bridges: D:P.51

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

EDO.7: 8 residues within 4Å: Chain C: G.43, P.44, Q.45, T.79 Chain D: G.43, P.44, Q.45, T.79 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:G.43, C:Q.45, C:Q.45, D:G.43, D:G.43, D:Q.45, D:Q.45 Water bridges: C:G.43

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
CCC

D
DDD

PA-I galactophilic lectin

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