SMTL ID : 8aij.1

STRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA STRAIN PAO1 IN COMPLEX WITH N-(alpha-L-Fucopyranosyl)benzamide (6)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 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, M9I.3 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.2: 6 residues within 4Å: Chain A: E.95, D.99, D.101, D.104 Ligands: CA.1, M9I.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.7: 6 residues within 4Å: Chain B: E.95, D.99, D.101, D.104 Ligands: CA.8, M9I.9 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.8: 7 residues within 4Å: Chain A: G.114 Chain B: N.21, D.101, N.103, D.104 Ligands: CA.7, M9I.9 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.11: 7 residues within 4Å: Chain C: N.21, D.101, N.103, D.104 Chain D: G.114 Ligands: CA.12, M9I.13 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 C: E.95, D.99, D.101, D.104 Ligands: CA.11, M9I.13 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.14: 7 residues within 4Å: Chain C: G.114 Chain D: N.21, D.101, N.103, D.104 Ligands: CA.15, M9I.16 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.15: 6 residues within 4Å: Chain D: E.95, D.99, D.101, D.104 Ligands: CA.14, M9I.16 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

4 x M9I: N-(alpha-L-Fucopyranosyl)benzamide(Non-covalent)

M9I.3: 12 residues within 4Å: Chain A: N.21, S.22, S.23, E.95, D.96, T.98, D.99, D.101, D.104 Chain B: G.114 Ligands: CA.1, CA.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.23, A:D.96, A:D.101, A:D.101, A:D.104 Water bridges: A:S.22, A:S.23, A:S.23, A:D.99, A:D.101 M9I.9: 12 residues within 4Å: Chain A: G.114 Chain B: N.21, S.22, S.23, E.95, D.96, G.97, D.99, D.101, D.104 Ligands: CA.7, CA.8 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.23, B:D.96, A:G.114 Water bridges: B:S.22 M9I.13: 13 residues within 4Å: Chain C: N.21, S.22, S.23, E.95, D.96, G.97, T.98, D.99, D.101, D.104 Chain D: G.114 Ligands: CA.11, CA.12 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.23, C:D.96, C:D.99, D:G.114 Water bridges: C:S.22, C:S.23, C:S.23, C:D.99, C:D.99, C:D.99 M9I.16: 12 residues within 4Å: Chain C: G.114 Chain D: N.21, S.22, S.23, E.95, D.96, G.97, D.99, D.101, D.104 Ligands: CA.14, CA.15 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.23, D:D.96, D:D.99, C:G.114 Water bridges: D:S.22, D:S.23, D:S.23, D:D.99

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 2 residues within 4Å: Chain A: N.70, G.71 No protein-ligand interaction detected (PLIP) EDO.5: 1 residues within 4Å: Chain A: N.34 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.34 EDO.6: 5 residues within 4Å: Chain A: N.29, Q.66, V.67, S.68, P.73 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.29 Water bridges: A:V.67, A:V.67 EDO.10: 1 residues within 4Å: Chain B: T.7 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.7, B:T.7 Water bridges: C:N.85

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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