SMTL ID : 5maz.1

STRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA STRAIN PA14 IN COMPLEX WITH 3-Thiophenesulfonamide-2,5-dimethyl-N-methyl-beta-L-fucopyranoside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-tetramer

Ligands

8 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.7: 7 residues within 4Å: Chain A: G.114 Chain B: N.21, D.101, N.103, D.104 Ligands: FUL.5, CA.8 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.8: 6 residues within 4Å: Chain B: E.95, D.99, D.101, D.104 Ligands: FUL.5, CA.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.10: 6 residues within 4Å: Chain C: E.95, D.99, D.101, D.104 Ligands: CA.11, FUL.12 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.11: 7 residues within 4Å: Chain C: N.21, D.101, N.103, D.104 Chain D: G.114 Ligands: CA.10, FUL.12 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.16: 7 residues within 4Å: Chain C: G.114 Chain D: N.21, D.101, N.103, D.104 Ligands: FUL.14, CA.17 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.17: 6 residues within 4Å: Chain D: E.95, D.99, D.101, D.104 Ligands: FUL.14, CA.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 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, IGF.4 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.23, A:D.96, B:G.114 Water bridges: A:D.99 FUL.5: 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: IGF.6, CA.7, CA.8 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.23, B:D.96, A:G.114 FUL.12: 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.10, CA.11, IGF.13 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:A.23, C:D.96, C:D.104, D:G.114 FUL.14: 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: IGF.15, CA.16, CA.17 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:A.23, D:D.96, D:D.99, D:D.104, C:G.114

4 x IGF: N,2,5-trimethyl-3-thiophenesulfonamide(Non-covalent)

IGF.4: 7 residues within 4Å: Chain A: S.22, A.23, G.24, N.70, D.96, S.97 Ligands: FUL.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.23 Hydrogen bonds: A:D.96, A:S.97 IGF.6: 7 residues within 4Å: Chain B: S.22, A.23, G.24, V.69, D.96, S.97 Ligands: FUL.5 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.69 Water bridges: B:S.97, B:S.97 IGF.13: 9 residues within 4Å: Chain C: S.22, A.23, G.24, V.69, N.70, R.72, D.96, S.97 Ligands: FUL.12 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.69 Hydrogen bonds: C:D.96, C:S.97 IGF.15: 8 residues within 4Å: Chain D: S.22, A.23, G.24, V.69, D.96, S.97 Ligands: FUL.14, GOL.18 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:V.69 Hydrogen bonds: D:D.96, D:S.97

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

EDO.9: 6 residues within 4Å: Chain B: A.1, Q.3, L.76 Chain D: A.1, Q.3, L.76 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:A.1, D:A.1, D:A.1 Water bridges: B:A.1

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.18: 5 residues within 4Å: Chain D: A.23, G.24, T.25, Q.43 Ligands: IGF.15 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.25, D:T.25 Water bridges: D:T.25, D:N.70, D:N.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sommer, R. et al., Discovery of a new class of C-glycoside based inhibitors of the virulence factor LecB from Pseudomonas aeruginosa. To Be Published

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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