SMTL ID : 3zdv.1

Crystal structure of the LecB lectin from Pseudomonas aeruginosa in complex with Methyl 6-(2,4,6-trimethylphenylsulfonylamido)-6-deoxy-alpha-D-mannopyranoside

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

homo-tetramer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: E.96, D.100, D.102, D.105 Ligands: CA.2, MMA.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.96, A:E.96, A:D.100, A:D.102, A:D.105 CA.2: 7 residues within 4Å: Chain A: N.22, D.102, N.104, D.105 Chain B: G.115 Ligands: CA.1, MMA.3 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Metal complexes: B:G.115, A:N.22, A:D.102, A:D.105 CA.5: 6 residues within 4Å: Chain B: E.96, D.100, D.102, D.105 Ligands: CA.6, MMA.7 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.96, B:E.96, B:D.100, B:D.102, B:D.105 CA.6: 7 residues within 4Å: Chain A: G.115 Chain B: N.22, D.102, N.104, D.105 Ligands: CA.5, MMA.7 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Metal complexes: B:N.22, B:D.102, B:D.105, A:G.115 CA.11: 6 residues within 4Å: Chain C: E.96, D.100, D.102, D.105 Ligands: CA.12, MMA.13 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.96, C:E.96, C:D.100, C:D.102, C:D.105 CA.12: 7 residues within 4Å: Chain C: N.22, D.102, N.104, D.105 Chain D: G.115 Ligands: CA.11, MMA.13 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Metal complexes: C:N.22, C:D.102, C:D.102, C:D.105, D:G.115 CA.15: 6 residues within 4Å: Chain D: E.96, D.100, D.102, D.105 Ligands: CA.16, MMA.17 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.96, D:E.96, D:D.100, D:D.102, D:D.105 CA.16: 7 residues within 4Å: Chain C: G.115 Chain D: N.22, D.102, N.104, D.105 Ligands: CA.15, MMA.17 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Metal complexes: C:G.115, D:N.22, D:D.102, D:D.105

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

MMA.3: 13 residues within 4Å: Chain A: N.22, S.23, S.24, E.96, D.97, G.98, D.100, D.102, D.105 Chain B: G.115 Ligands: CA.1, CA.2, F1A.4 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.24, A:D.100, A:D.105, A:D.105, B:G.115 Water bridges: A:D.100 MMA.7: 12 residues within 4Å: Chain A: G.115 Chain B: N.22, S.23, S.24, E.96, D.97, D.100, D.102, D.105 Ligands: CA.5, CA.6, F1A.8 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.115, B:S.24, B:D.100, B:D.105 Water bridges: B:D.100 MMA.13: 12 residues within 4Å: Chain C: N.22, S.23, S.24, E.96, D.97, D.100, D.102, D.105 Chain D: G.115 Ligands: CA.11, CA.12, F1A.14 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.24, C:D.100, C:D.105, D:G.115 MMA.17: 12 residues within 4Å: Chain C: G.115 Chain D: N.22, S.23, S.24, E.96, D.97, D.100, D.102, D.105 Ligands: CA.15, CA.16, F1A.18 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:G.115, D:S.24, D:D.100, D:D.105

4 x F1A: 2,4,6-trimethylbenzenesulfonamide(Non-covalent)

F1A.4: 6 residues within 4Å: Chain A: S.24, G.25, N.71, D.97, G.98 Ligands: MMA.3 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.96, A:T.99 F1A.8: 4 residues within 4Å: Chain B: G.25, D.97, G.98 Ligands: MMA.7 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.96, B:T.99 F1A.14: 6 residues within 4Å: Chain C: S.24, V.70, N.71, D.97, G.98 Ligands: MMA.13 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.70 Water bridges: C:E.96, C:T.99 F1A.18: 5 residues within 4Å: Chain D: S.24, G.25, V.70, D.97 Ligands: MMA.17 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.70

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 2 residues within 4Å: Chain B: Q.54, V.55 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.55 Water bridges: B:V.55

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

EDO.10: 5 residues within 4Å: Chain B: A.2, Q.4 Chain D: A.2, Q.4, L.77 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:A.2, D:L.77, B:A.2 Water bridges: D:A.2, D:A.2

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.19: 3 residues within 4Å: Chain D: S.45, T.46, N.47 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.46, D:T.46, D:T.46, D:N.47 Water bridges: D:Q.44, D:Q.44, D:N.47

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Hauck, D. et al., Discovery of Two Classes of Potent Glycomimetic Inhibitors of Pseudomonas Aeruginosa Lecb with Distinct Binding Modes. Acs Chem.Biol. (2013)

Release Date

2013-09-18

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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