SMTL ID : 5mb1.1

STRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA STRAIN PA14 IN COMPLEX WITH 2,4,6-Trimethylphenylsulfonamide-N-methyl-L-fucopyranoside

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

7 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: E.95, D.99, D.101, D.104 Ligands: CA.2, FUL.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.2: 7 residues within 4Å: Chain A: N.21, D.101, N.103, D.104 Chain B: G.114 Ligands: CA.1, FUL.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.5: 6 residues within 4Å: Chain B: E.95, D.99, D.101, D.104 Ligands: CA.6, FUL.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.6: 7 residues within 4Å: Chain A: G.114 Chain B: N.21, D.101, N.103, D.104 Ligands: CA.5, FUL.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.9: 5 residues within 4Å: Chain C: N.21, D.99, N.103, D.104 Chain D: G.114 5 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:G.114, C:N.21, C:D.99, C:D.104, H2O.20 CA.10: 6 residues within 4Å: Chain D: E.95, D.99, D.101, D.104 Ligands: CA.11, FUL.12 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.11: 7 residues within 4Å: Chain C: G.114 Chain D: N.21, D.101, N.103, D.104 Ligands: CA.10, FUL.12 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:N.21, D:D.101, D:D.104, C:G.114, H2O.14

3 x FUL: beta-L-fucopyranose(Non-covalent)

FUL.3: 13 residues within 4Å: Chain A: N.21, S.22, A.23, E.95, D.96, S.97, D.99, D.101, D.104 Chain B: G.114 Ligands: CA.1, CA.2, 7KT.4 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.23, A:D.96, A:D.104, B:G.114 FUL.7: 13 residues within 4Å: Chain A: G.114 Chain B: N.21, S.22, A.23, E.95, D.96, S.97, D.99, D.101, D.104 Ligands: CA.5, CA.6, 7KT.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.23, B:D.96, B:D.99, B:D.101 FUL.12: 14 residues within 4Å: Chain C: G.114 Chain D: N.21, S.22, A.23, T.45, E.95, D.96, S.97, D.99, D.101, D.104 Ligands: CA.10, CA.11, 7KT.13 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:A.23, D:T.45 Hydrogen bonds: D:A.23, D:D.96, D:D.101

3 x 7KT: ~{N},2,4,6-tetramethylbenzenesulfonamide(Non-covalent)

7KT.4: 8 residues within 4Å: Chain A: S.22, A.23, G.24, V.69, R.72, D.96, S.97 Ligands: FUL.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.69 Water bridges: A:S.97 7KT.8: 7 residues within 4Å: Chain B: S.22, A.23, G.24, V.69, D.96, S.97 Ligands: FUL.7 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.69 7KT.13: 6 residues within 4Å: Chain D: S.22, A.23, G.24, D.96, S.97 Ligands: FUL.12 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.97, D:S.97 Water bridges: D:A.23

1 x FLC: CITRATE ANION(Non-covalent)

FLC.14: 4 residues within 4Å: Chain D: Q.31, N.34, K.62, Q.64 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:Q.31, D:N.34, D:N.34, D:K.62, D:Q.64, D:Q.64 Water bridges: D:N.34 Salt bridges: D:K.62, D:K.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sommer, R. et al., Glycomimetic, Orally Bioavailable LecB Inhibitors Block Biofilm Formation of Pseudomonas aeruginosa. J. Am. Chem. Soc. (2018)

Release Date

2017-12-20

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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