SMTL ID : 8ri7.1

Beta-galactosidase (LacZ) in complex with galactosyrin from Pseudomonas syringae.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x 01: (2S,3R,4S)-2-[bis(oxidanyl)methyl]pyrrolidine-3,4-diol

01.1: 15 residues within 4Å: Chain A: N.103, D.202, H.392, N.461, E.462, M.503, Y.504, E.538, H.541, W.569, F.602, N.605, W.1000 Ligands: MG.2, NA.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.202, A:N.461, A:E.462, A:E.462, A:E.538 Water bridges: A:N.103, A:D.202, A:D.202, A:D.202 Salt bridges: A:H.392 01.6: 15 residues within 4Å: Chain B: N.103, D.202, H.392, N.461, E.462, M.503, Y.504, E.538, H.541, W.569, F.602, N.605, W.1000 Ligands: MG.7, NA.9 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.461, B:E.462, B:E.462, B:Y.504, B:E.538 Water bridges: B:N.103, B:D.202, B:D.202, B:D.202, B:E.462 Salt bridges: B:H.392 01.11: 15 residues within 4Å: Chain C: N.103, D.202, H.392, N.461, E.462, M.503, Y.504, E.538, H.541, W.569, F.602, N.605, W.1000 Ligands: MG.12, NA.14 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:D.202, C:N.461, C:E.462, C:E.462, C:E.538 Water bridges: C:N.103, C:D.202, C:D.202, C:D.202 Salt bridges: C:H.392 01.16: 15 residues within 4Å: Chain D: N.103, D.202, H.392, N.461, E.462, M.503, Y.504, E.538, H.541, W.569, F.602, N.605, W.1000 Ligands: MG.17, NA.19 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:N.461, D:E.462, D:E.462, D:Y.504, D:E.538 Water bridges: D:N.103, D:D.202, D:D.202, D:D.202, D:E.462 Salt bridges: D:H.392

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: E.417, H.419, E.462 Ligands: 01.1 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.417, A:H.419, A:E.462, H2O.4, H2O.8, H2O.9 MG.3: 5 residues within 4Å: Chain A: D.16, N.19, V.22, Q.164, D.194 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.16, A:N.19, A:V.22, A:D.194 MG.7: 4 residues within 4Å: Chain B: E.417, H.419, E.462 Ligands: 01.6 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.417, B:H.419, B:E.462, H2O.13, H2O.17, H2O.19 MG.8: 5 residues within 4Å: Chain B: D.16, N.19, V.22, Q.164, D.194 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.16, B:N.19, B:V.22, B:D.194 MG.12: 4 residues within 4Å: Chain C: E.417, H.419, E.462 Ligands: 01.11 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.417, C:H.419, C:E.462, H2O.23, H2O.27, H2O.29 MG.13: 5 residues within 4Å: Chain C: D.16, N.19, V.22, Q.164, D.194 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.16, C:N.19, C:V.22, C:D.194 MG.17: 4 residues within 4Å: Chain D: E.417, H.419, E.462 Ligands: 01.16 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.417, D:H.419, D:E.462, H2O.33, H2O.37, H2O.38 MG.18: 5 residues within 4Å: Chain D: D.16, N.19, V.22, Q.164, D.194 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.16, D:N.19, D:V.22, D:D.194

8 x NA: SODIUM ION(Non-functional Binders)

NA.4: 5 residues within 4Å: Chain A: Y.101, D.202, F.602, N.605 Ligands: 01.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.202, A:N.605 NA.5: 4 residues within 4Å: Chain A: F.557, Y.560, P.561, L.563 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.557, A:L.563 NA.9: 5 residues within 4Å: Chain B: Y.101, D.202, F.602, N.605 Ligands: 01.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.202, B:N.605 NA.10: 4 residues within 4Å: Chain B: F.557, Y.560, P.561, L.563 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.561, B:L.563 NA.14: 5 residues within 4Å: Chain C: Y.101, D.202, F.602, N.605 Ligands: 01.11 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.202, C:N.605 NA.15: 4 residues within 4Å: Chain C: F.557, Y.560, P.561, L.563 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.560, C:L.563 NA.19: 5 residues within 4Å: Chain D: Y.101, D.202, F.602, N.605 Ligands: 01.16 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:F.602, D:N.605 NA.20: 4 residues within 4Å: Chain D: F.557, Y.560, P.561, L.563 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:F.557, D:L.563

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hardenbrook, N.J. et al., Identification of a novel inhibitor for beta-galactosidase from Pseudomonas syringae. To Be Published

Release Date

2025-01-01

Peptides

Beta-galactosidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Beta-galactosidase

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