SMTL ID : 5may.1

STRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA STRAIN PA14 IN COMPLEX WITH 2-Thiophenesulfonamide-N-(beta-L-fucopyranosyl methyl)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 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, 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.2: 7 residues within 4Å: Chain A: E.95, D.96, D.99, D.101, D.104 Ligands: CA.1, 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.5: 7 residues within 4Å: Chain A: G.114 Chain B: N.21, D.101, N.103, D.104 Ligands: CA.6, FUL.7 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Metal complexes: A:G.114, B:N.21, B:D.101, B:D.104 CA.6: 6 residues within 4Å: Chain B: E.95, D.99, D.101, D.104 Ligands: CA.5, 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.9: 7 residues within 4Å: Chain C: N.21, D.101, N.103, D.104 Chain D: G.114 Ligands: CA.10, FUL.11 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.10: 6 residues within 4Å: Chain C: E.95, D.99, D.101, D.104 Ligands: CA.9, FUL.11 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.13: 7 residues within 4Å: Chain C: G.114 Chain D: N.21, D.101, N.103, D.104 Ligands: CA.14, FUL.15 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.14: 7 residues within 4Å: Chain D: E.95, D.96, D.99, D.101, D.104 Ligands: CA.13, FUL.15 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 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, PK6.4 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.23, A:D.96, A:D.101, 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, PK6.8 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.114, B:A.23, B:D.96, B:D.104 FUL.11: 13 residues within 4Å: Chain C: N.21, S.22, A.23, E.95, D.96, S.97, D.99, D.101, D.104 Chain D: G.114 Ligands: CA.9, CA.10, PK6.12 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:A.23 Hydrogen bonds: C:A.23, C:D.96, C:D.101 Water bridges: C:T.98 FUL.15: 13 residues within 4Å: Chain C: G.114 Chain D: N.21, S.22, A.23, E.95, D.96, S.97, D.99, D.101, D.104 Ligands: CA.13, CA.14, PK6.16 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:A.23 Hydrogen bonds: D:A.23, D:D.96, D:D.101, D:D.101

4 x PK6: N-methyl-2-thiophenesulfonamide(Non-covalent)

PK6.4: 6 residues within 4Å: Chain A: S.22, A.23, G.24, D.96, S.97 Ligands: FUL.3 No protein-ligand interaction detected (PLIP) PK6.8: 7 residues within 4Å: Chain B: S.22, A.23, G.24, R.72, D.96, S.97 Ligands: FUL.7 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.97 PK6.12: 6 residues within 4Å: Chain C: S.22, A.23, G.24, R.72, D.96 Ligands: FUL.11 No protein-ligand interaction detected (PLIP) PK6.16: 6 residues within 4Å: Chain D: S.22, A.23, G.24, D.96, S.97 Ligands: FUL.15 No protein-ligand interaction detected (PLIP)

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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