SMTL ID : 5a3o.1

Crystal structure of the LecB lectin from Pseudomonas aeruginosa in complex with Methyl 6-(cinnamido)-6-deoxy-alpha-D-mannopyranoside at 1.6 ansgtrom

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 7 residues within 4Å: Chain A: E.95, D.96, D.99, D.101, D.104 Ligands: CA.2, MMA.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, MMA.3 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Metal complexes: A:N.21, A:D.101, A:D.101, A:D.104, B:G.114 CA.6: 6 residues within 4Å: Chain B: E.95, D.99, D.101, D.104 Ligands: CA.7, MMA.8 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.7: 7 residues within 4Å: Chain A: G.114 Chain B: N.21, D.101, N.103, D.104 Ligands: CA.6, MMA.8 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: E.95, D.96, D.99, D.101, D.104 Ligands: CA.12, MMA.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.12: 7 residues within 4Å: Chain C: N.21, D.101, N.103, D.104 Chain D: G.114 Ligands: CA.11, MMA.13 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Metal complexes: D:G.114, C:N.21, C:D.101, C:D.104 CA.16: 6 residues within 4Å: Chain D: E.95, D.99, D.101, D.104 Ligands: CA.17, MMA.18 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.17: 7 residues within 4Å: Chain C: G.114 Chain D: N.21, D.101, N.103, D.104 Ligands: CA.16, MMA.18 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Metal complexes: D:N.21, D:D.101, D:D.101, D:D.104, C:G.114

4 x MMA: methyl alpha-D-mannopyranoside(Non-covalent)

MMA.3: 13 residues within 4Å: Chain A: N.21, S.22, S.23, E.95, D.96, G.97, D.99, D.101, D.104 Chain B: G.114 Ligands: CA.1, CA.2, DH6.4 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.23, A:D.101, A:D.104, A:D.104, B:G.114 MMA.8: 13 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.6, CA.7, DH6.9 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.23, B:D.99, B:D.104, A:G.114 Water bridges: B:D.99 MMA.13: 12 residues within 4Å: Chain C: N.21, S.22, S.23, E.95, D.96, D.99, D.101, D.104 Chain D: G.114 Ligands: CA.11, CA.12, DH6.14 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.23, C:D.101, C:D.104, D:G.114 Water bridges: C:D.99 MMA.18: 12 residues within 4Å: Chain C: G.114 Chain D: N.21, S.22, S.23, E.95, D.96, D.99, D.101, D.104 Ligands: CA.16, CA.17, DH6.19 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:G.114, D:S.23, D:D.99, D:D.104 Water bridges: D:D.99

4 x DH6: CINNAMIDE(Non-covalent)

DH6.4: 3 residues within 4Å: Chain A: S.23, G.24 Ligands: MMA.3 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.22, A:S.22 DH6.9: 4 residues within 4Å: Chain B: D.96, G.97, T.98 Ligands: MMA.8 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.98 Hydrogen bonds: B:D.96 DH6.14: 2 residues within 4Å: Chain C: S.23 Ligands: MMA.13 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.23 Water bridges: C:T.98, C:T.98 DH6.19: 2 residues within 4Å: Chain D: S.23 Ligands: MMA.18 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.23 Water bridges: D:T.98, D:T.98

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 6 residues within 4Å: Chain A: Q.3, F.6, S.78, A.79 Chain D: T.84, N.85 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain B: Q.3, F.6, S.78, A.79 Chain C: T.84, N.85 Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain B: T.84, N.85 Chain C: Q.3, F.6, S.78, A.79 Ligand excluded by PLIP CL.20: 6 residues within 4Å: Chain A: T.84, N.85 Chain D: Q.3, F.6, S.78, A.79 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sommer, R. et al., Cinnamide Derivatives of D-Mannose as Inhibitors of the Bacterial Virulence Factor Lecb from Pseudomonas Aeruginosa. Chemistryopen (2015)

Release Date

2015-07-22

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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