SMTL ID : 9g3s.1 (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

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

YIO-FUC.1: 12 residues within 4Å: Chain A: N.21, S.22, S.23, G.24, E.95, D.96, D.99, D.101, D.104 Chain B: G.114 Ligands: CA.5, CA.6 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.23, A:D.96, A:D.99, B:G.114, A:N.70 YIO-FUC.3: 16 residues within 4Å: Chain C: N.21, S.22, S.23, G.24, V.69, R.72, E.95, D.96, G.97, D.99, D.101, D.104 Chain D: G.114 Ligands: CA.14, CA.15, SO4.18 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:G.114, C:S.23, C:D.96, C:D.99, C:S.22, C:G.24, C:R.72 Water bridges: C:D.96 YIO-FUC.4: 13 residues within 4Å: Chain C: G.114 Chain D: N.21, S.22, S.23, G.24, N.70, E.95, D.96, D.99, D.101, D.104 Ligands: CA.21, CA.22 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.23, D:D.96, D:D.99, D:D.104, C:G.114, D:N.70

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

FUC-YIO.2: 12 residues within 4Å: Chain A: G.114 Chain B: N.21, S.22, S.23, G.24, E.95, D.96, D.99, D.101, D.104 Ligands: CA.10, CA.11 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.114, B:S.23, B:D.96, B:D.99, B:D.104

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 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.10: 7 residues within 4Å: Chain B: E.95, D.96, D.99, D.101, D.104 Ligands: FUC-YIO.2, CA.11 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.11: 7 residues within 4Å: Chain A: G.114 Chain B: N.21, D.101, N.103, D.104 Ligands: FUC-YIO.2, CA.10 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.14: 6 residues within 4Å: Chain C: E.95, D.99, D.101, D.104 Ligands: YIO-FUC.3, CA.15 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.15: 7 residues within 4Å: Chain C: N.21, D.101, N.103, D.104 Chain D: G.114 Ligands: YIO-FUC.3, CA.14 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Metal complexes: D:G.114, C:N.21, C:D.101, C:D.101, C:D.104 CA.21: 6 residues within 4Å: Chain D: E.95, D.99, D.101, D.104 Ligands: YIO-FUC.4, CA.22 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.22: 7 residues within 4Å: Chain C: G.114 Chain D: N.21, D.101, N.103, D.104 Ligands: YIO-FUC.4, CA.21 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

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

SO4.7: 3 residues within 4Å: Chain A: N.33, G.58, S.59 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.33, A:S.59, A:S.59 Water bridges: A:S.60, A:S.60 SO4.8: 2 residues within 4Å: Chain A: P.9, A.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.10 SO4.9: 2 residues within 4Å: Chain A: T.12, R.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.13 Salt bridges: A:R.13 SO4.12: 2 residues within 4Å: Chain B: A.1 Chain D: D.75 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:D.75, B:A.1 SO4.13: 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 SO4.16: 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 SO4.17: 3 residues within 4Å: Chain C: G.24, T.25, N.70 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.25, C:N.70 SO4.18: 3 residues within 4Å: Chain C: N.70, R.72 Ligands: YIO-FUC.3 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.70 Salt bridges: C:R.72 SO4.19: 3 residues within 4Å: Chain C: N.33, G.58, S.59 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.33, C:S.59, C:S.59 Water bridges: C:S.60, C:S.60 SO4.20: 4 residues within 4Å: Chain C: S.44, T.45, N.46, A.48 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.44, C:T.45, C:T.45, C:N.46, C:N.46 SO4.23: 3 residues within 4Å: Chain D: N.11, T.12, R.13 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.13 Water bridges: D:L.113 Salt bridges: D:R.13

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
A

B
B

C
C

D
D

Fucose-binding lectin PA-IIL

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