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: 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.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: 1 interactions with chain C, 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:G.114, D:N.21, D:D.101, D:D.104, 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   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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