SMTL ID : 9g3s.2 (1 other biounit)

LecB from Pseudomonas aeruginosa in complex with a synthetic thiofucoside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

4 x YIO- FUC: alpha-L-fucopyranose-(1-1)-1-thio-beta-D-galactopyranose(Non-covalent)

YIO-FUC.1: 15 residues within 4Å: Chain A: N.21, S.22, S.23, G.24, R.72, E.95, D.96, G.97, D.99, D.101, D.104 Chain B: G.114 Ligands: CA.5, CA.6, SO4.8 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.23, A:D.96, A:D.99, A:D.104, B:G.114, A:R.72 YIO-FUC.2: 13 residues within 4Å: Chain A: G.114 Chain B: N.21, S.22, S.23, G.24, N.70, E.95, D.96, D.99, D.101, D.104 Ligands: CA.12, CA.13 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.23, B:D.96, B:D.99, A:G.114, B:N.70 YIO-FUC.3: 14 residues within 4Å: Chain C: N.21, S.22, S.23, G.24, V.69, R.72, E.95, D.96, D.99, D.101, D.104 Chain D: G.114 Ligands: CA.17, CA.18 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.23, C:D.96, C:D.99, D:G.114, C:S.22, C:G.24 YIO-FUC.4: 14 residues within 4Å: Chain C: G.114 Chain D: N.21, S.22, S.23, G.24, V.69, N.70, E.95, D.96, D.99, D.101, D.104 Ligands: CA.20, CA.21 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.23, D:D.96, D:D.99, D:D.101, D:N.70

8 x CA: CALCIUM ION(Non-covalent)

CA.5: 6 residues within 4Å: Chain A: E.95, D.99, D.101, D.104 Ligands: YIO-FUC.1, CA.6 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.6: 7 residues within 4Å: Chain A: N.21, D.101, N.103, D.104 Chain B: G.114 Ligands: YIO-FUC.1, CA.5 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Metal complexes: B:G.114, A:N.21, A:D.101, A:D.104 CA.12: 6 residues within 4Å: Chain B: E.95, D.99, D.101, D.104 Ligands: YIO-FUC.2, CA.13 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.13: 7 residues within 4Å: Chain A: G.114 Chain B: N.21, D.101, N.103, D.104 Ligands: YIO-FUC.2, CA.12 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Metal complexes: B:N.21, B:D.101, B:D.104, A:G.114 CA.17: 6 residues within 4Å: Chain C: E.95, D.99, D.101, D.104 Ligands: YIO-FUC.3, CA.18 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.18: 7 residues within 4Å: Chain C: N.21, D.101, N.103, D.104 Chain D: G.114 Ligands: YIO-FUC.3, CA.17 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.20: 6 residues within 4Å: Chain D: E.95, D.99, D.101, D.104 Ligands: YIO-FUC.4, CA.21 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.21: 7 residues within 4Å: Chain C: G.114 Chain D: N.21, D.101, N.103, D.104 Ligands: YIO-FUC.4, CA.20 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

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

SO4.7: 3 residues within 4Å: Chain A: N.33, G.58, S.59 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.33, A:S.59 Water bridges: A:S.60, A:S.60 SO4.8: 2 residues within 4Å: Chain A: R.72 Ligands: YIO-FUC.1 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.72 SO4.9: 3 residues within 4Å: Chain A: T.45, N.46 Chain B: R.13 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.13 Hydrogen bonds: A:T.45, A:T.45 SO4.10: 3 residues within 4Å: Chain A: N.11, T.12, R.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.13 SO4.11: 2 residues within 4Å: Chain A: P.9, A.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.10 SO4.14: 4 residues within 4Å: Chain B: S.44, T.45, N.46, A.48 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.44, B:T.45, B:N.46, B:N.46 SO4.15: 3 residues within 4Å: Chain B: N.33, G.58, S.59 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.33, B:S.59, B:S.59 Water bridges: B:S.60 SO4.16: 3 residues within 4Å: Chain B: N.11, T.12, R.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.13 SO4.19: 3 residues within 4Å: Chain C: N.11, T.12, R.13 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.13 SO4.22: 2 residues within 4Å: Chain D: T.12, R.13 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.13 Water bridges: D:R.13, D:R.13, D:L.113 Salt bridges: D:R.13 SO4.23: 3 residues within 4Å: Chain D: N.33, G.58, S.59 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.33, D:S.59 Water bridges: D:S.60, D:S.60 SO4.24: 3 residues within 4Å: Chain D: S.44, T.45, N.46 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.45, D:N.46, D:N.46 SO4.25: 3 residues within 4Å: Chain D: G.24, T.25, N.70 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.25, D:T.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Faltinek, L. et al., Bispecific Thio-linked Disaccharides as Inhibitors of Pseudomonas aeruginosa Lectins LecA (PA-IL) and LecB (PA-IIL): Dual-Targeting Strategy. Chemistry (2024)

Release Date

2024-11-27

Peptides

Fucose-binding lectin PA-IIL: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

Fucose-binding lectin PA-IIL

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