SMTL ID : 8aiy.1

STRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA STRAIN PAO1 IN COMPLEX WITH N-(beta-L-Fucopyranosyl)-biphenyl-3-carboxamide (4i)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-tetramer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 7 residues within 4Å: Chain A: N.21, D.101, N.103, D.104 Chain B: G.114 Ligands: CA.2, MJO.3 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Metal complexes: A:N.21, A:D.101, A:D.104, B:G.114 CA.2: 6 residues within 4Å: Chain A: E.95, D.99, D.101, D.104 Ligands: CA.1, MJO.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.5: 7 residues within 4Å: Chain A: G.114 Chain B: N.21, D.101, N.103, D.104 Ligands: CA.6, MJO.7 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.6: 6 residues within 4Å: Chain B: E.95, D.99, D.101, D.104 Ligands: CA.5, MJO.7 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.9: 6 residues within 4Å: Chain C: E.95, D.99, D.101, D.104 Ligands: MJO.8, CA.10 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.10: 7 residues within 4Å: Chain C: N.21, D.101, N.103, D.104 Chain D: G.114 Ligands: MJO.8, CA.9 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Metal complexes: C:N.21, C:D.101, C:D.104, D:G.114 CA.12: 6 residues within 4Å: Chain D: E.95, D.99, D.101, D.104 Ligands: CA.13, MJO.14 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.13: 7 residues within 4Å: Chain C: G.114 Chain D: N.21, D.101, N.103, D.104 Ligands: CA.12, MJO.14 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

4 x MJO: N-(beta-L-Fucopyranosyl)-biphenyl-3-carboxamide(Non-covalent)

MJO.3: 15 residues within 4Å: Chain A: N.21, S.22, S.23, G.24, V.69, N.70, E.95, D.96, G.97, D.99, D.101, D.104 Chain B: G.114 Ligands: CA.1, CA.2 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.69, A:D.96 Hydrogen bonds: A:S.22, A:S.23, A:D.99, A:D.104, B:G.114 Water bridges: A:S.23, A:T.98, A:D.99 MJO.7: 14 residues within 4Å: Chain A: G.114 Chain B: N.21, S.22, S.23, G.24, V.69, N.70, E.95, D.96, D.99, D.101, D.104 Ligands: CA.5, CA.6 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.69 Hydrogen bonds: B:S.23, B:G.24, B:D.96, B:D.99, B:D.104, A:G.114 Water bridges: B:S.23, B:S.23 MJO.8: 16 residues within 4Å: Chain C: 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 Chain D: G.114 Ligands: CA.9, CA.10 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:D.96, C:D.99, C:D.104, D:G.114 Water bridges: C:D.99 MJO.14: 15 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, G.97, D.99, D.101, D.104 Ligands: CA.12, CA.13 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.69 Hydrogen bonds: D:S.23, D:D.96, D:D.99, D:D.104, C:G.114 Water bridges: D:S.23, D:S.23, D:D.99

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

SO4.4: 4 residues within 4Å: Chain A: S.44, T.45, N.46, A.48 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.45, A:N.46, A:N.46 Water bridges: A:Q.43 SO4.11: 3 residues within 4Å: Chain C: S.44, T.45, N.46 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.44, C:T.45, C:T.45, C:N.46 Water bridges: C:Q.43, C:Q.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mala, P. et al., Discovery of N -beta-l-Fucosyl Amides as High-Affinity Ligands for the Pseudomonas aeruginosa Lectin LecB. J.Med.Chem. (2022)

Release Date

2022-11-02

Peptides

Fucose-binding lectin PA-IIL: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

C
CCC

D
DDD

Fucose-binding lectin PA-IIL

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