SMTL ID : 9g3k.1

LecB from PA01 in complex with synthetic beta - fucosylamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-tetramer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: N.21, D.101, N.103, D.104 Chain B: G.114 Ligands: CA.2 5 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:G.114, A:N.21, A:D.101, A:D.104, H2O.1 CA.2: 5 residues within 4Å: Chain A: E.95, D.99, D.101, D.104 Ligands: CA.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.95, A:D.99, A:D.104, A:D.104, H2O.1 CA.4: 6 residues within 4Å: Chain A: G.114 Chain B: N.21, D.101, N.103, D.104 Ligands: CA.5 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:N.21, B:D.101, B:D.104, A:G.114, H2O.1 CA.5: 6 residues within 4Å: Chain B: E.95, D.99, D.101, D.104 Ligands: CA.4, SO4.6 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.95, B:E.95, B:D.99, B:D.104, B:D.104 CA.7: 6 residues within 4Å: Chain C: N.21, D.101, N.103, D.104 Chain D: G.114 Ligands: CA.8 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:N.21, C:D.101, C:D.104, D:G.114, H2O.17 CA.8: 5 residues within 4Å: Chain C: E.95, D.99, D.101, D.104 Ligands: CA.7 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.95, C:E.95, C:D.99, C:D.104, C:D.104 CA.11: 7 residues within 4Å: Chain C: G.114 Chain D: N.21, D.101, N.103, D.104 Ligands: CA.12, R7E.13 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Metal complexes: D:N.21, D:D.101, D:D.104, C:G.114 CA.12: 6 residues within 4Å: Chain D: E.95, D.99, D.101, D.104 Ligands: CA.11, R7E.13 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

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: S.22, S.23, D.96, D.99 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.23, A:D.96 Water bridges: A:D.104 SO4.6: 3 residues within 4Å: Chain B: S.22, S.23 Ligands: CA.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.22, B:S.23 Water bridges: B:D.104 SO4.9: 4 residues within 4Å: Chain C: Q.43, S.44, N.46, A.48 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.43, C:S.44, C:N.46 Water bridges: C:N.46, C:N.46, C:N.46 SO4.10: 2 residues within 4Å: Chain C: S.22, S.23 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.23 Water bridges: C:N.21, C:S.22 SO4.14: 2 residues within 4Å: Chain D: G.58, S.59 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:S.59 Water bridges: D:N.11, D:N.11, D:N.33, D:N.33, D:S.59, D:S.59, D:S.59, D:S.59

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.13: 15 residues within 4Å: Chain C: G.114 Chain D: N.21, S.22, S.23, G.24, T.45, V.69, E.95, D.96, G.97, D.99, D.101, D.104 Ligands: CA.11, CA.12 11 PLIP interactions: 1 interactions with chain C, 10 interactions with chain D Hydrogen bonds: C:G.114, D:S.23, D:D.96, D:D.96, D:D.99 Hydrophobic interactions: D:T.45, D:V.69 Water bridges: D:S.23, 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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