SMTL ID : 9g3l.1

LecB from PA01 in complex with synthetic beta - fucosylamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-tetramer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: E.95, D.99, D.101, D.104 Ligands: CA.2, R7E.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.95, A:E.95, A:D.99, A:D.101, A:D.104 CA.2: 7 residues within 4Å: Chain A: N.21, D.101, N.103, D.104 Chain B: G.114 Ligands: CA.1, R7E.3 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Metal complexes: A:N.21, A:D.101, A:D.101, A:D.104, B:G.114 CA.4: 6 residues within 4Å: Chain B: E.95, D.99, D.101, D.104 Ligands: CA.5, 01.6 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.95, B:E.95, B:D.99, B:D.101, B:D.104 CA.5: 7 residues within 4Å: Chain A: G.114 Chain B: N.21, D.101, N.103, D.104 Ligands: CA.4, 01.6 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Metal complexes: A:G.114, B:N.21, B:D.101, B:D.101, B:D.104 CA.7: 6 residues within 4Å: Chain C: E.95, D.99, D.101, D.104 Ligands: CA.8, 01.9 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.95, C:E.95, C:D.99, C:D.101, C:D.104 CA.8: 7 residues within 4Å: Chain C: N.21, D.101, N.103, D.104 Chain D: G.114 Ligands: CA.7, 01.9 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Metal complexes: C:N.21, C:D.101, C:D.101, C:D.104, D:G.114 CA.10: 6 residues within 4Å: Chain D: E.95, D.99, D.101, D.104 Ligands: CA.11, 01.12 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.95, D:E.95, D:D.99, D:D.101, D:D.104 CA.11: 7 residues within 4Å: Chain C: G.114 Chain D: N.21, D.101, N.103, D.104 Ligands: CA.10, 01.12 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Metal complexes: C:G.114, D:N.21, D:D.101, D:D.104

1 x R7E: 5-[3-(aminomethyl)phenyl]-~{N}-[(2~{S},3~{S},4~{R},5~{S},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]furan-2-carboxamide(Non-covalent)

R7E.3: 15 residues within 4Å: Chain A: N.21, S.22, S.23, G.24, T.45, V.69, E.95, D.96, G.97, D.99, D.101, D.104 Chain B: G.114 Ligands: CA.1, CA.2 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.45, A:V.69 Hydrogen bonds: A:S.23, A:D.96, A:D.96, A:D.99, B:G.114 Water bridges: A:S.23, A:S.23, A:S.23, A:D.99

3 x 01: beta-L-fucopyranosyl-1H-indole-6-carboxamide

01.6: 16 residues within 4Å: Chain A: G.114 Chain B: N.21, S.22, S.23, G.24, T.45, V.69, N.70, E.95, D.96, G.97, D.99, D.101, D.104 Ligands: CA.4, CA.5 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.45, B:V.69 Hydrogen bonds: B:S.23, B:N.70, B:D.96, B:D.96, B:D.99, A:G.114 Water bridges: B:S.23, B:S.23, B:T.25 01.9: 15 residues within 4Å: Chain C: N.21, S.22, S.23, G.24, T.45, V.69, E.95, D.96, G.97, D.99, D.101, D.104 Chain D: G.114 Ligands: CA.7, CA.8 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:T.45, C:V.69 Hydrogen bonds: C:S.23, C:G.24, C:D.96, C:D.96, C:D.99, D:G.114 01.12: 13 residues within 4Å: Chain C: G.114 Chain D: N.21, S.22, S.23, G.24, V.69, E.95, D.96, D.99, D.101, D.104 Ligands: CA.10, CA.11 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.69 Hydrogen bonds: D:S.23, D:G.24, D:D.96, D:D.96, D:D.99, C:G.114 Water bridges: D:S.23, D:S.23, D:D.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Antonini, G. et al., Toward Dual-Target Glycomimetics against Two Bacterial Lectins to Fight Pseudomonas aeruginosa - Burkholderia cenocepacia Infections: A Biophysical Study. J.Med.Chem. (2025)

Release Date

2025-04-16

Peptides

Fucose-binding lectin PA-IIL: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Fucose-binding lectin PA-IIL

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