SMTL ID : 6tsh.1

Beta-galactosidase in complex with deoxygalacto-nojirimycin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.433, H.435, E.478 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.433, A:H.435, A:E.478, H2O.1, H2O.1, H2O.4 MG.3: 3 residues within 4Å: Chain B: E.433, H.435, E.478 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.433, B:H.435, B:E.478, H2O.9, H2O.10, H2O.12 MG.5: 3 residues within 4Å: Chain C: E.433, H.435, E.478 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.433, C:H.435, C:E.478, H2O.17, H2O.18, H2O.20 MG.7: 3 residues within 4Å: Chain D: E.433, H.435, E.478 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.433, D:H.435, D:E.478, H2O.26, H2O.26, H2O.29

4 x DGJ: (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol(Non-covalent)

DGJ.2: 11 residues within 4Å: Chain A: D.218, H.408, N.477, E.478, M.519, Y.520, E.554, H.557, W.585, F.618, N.621 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.218, A:H.408, A:N.477, A:E.478, A:Y.520, A:N.621 Water bridges: A:N.119, A:D.218, A:D.218, A:D.218 DGJ.4: 11 residues within 4Å: Chain B: D.218, H.408, N.477, E.478, M.519, Y.520, E.554, H.557, W.585, F.618, N.621 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.218, B:H.408, B:N.477, B:E.478, B:Y.520, B:N.621 Water bridges: B:N.119, B:D.218, B:D.218, B:D.218 DGJ.6: 11 residues within 4Å: Chain C: D.218, H.408, N.477, E.478, M.519, Y.520, E.554, H.557, W.585, F.618, N.621 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:H.408, C:N.477, C:E.478, C:Y.520, C:Y.520, C:N.621 Water bridges: C:N.119, C:D.218, C:D.218, C:D.218 DGJ.8: 11 residues within 4Å: Chain D: D.218, H.408, N.477, E.478, M.519, Y.520, E.554, H.557, W.585, F.618, N.621 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:H.408, D:N.477, D:E.478, D:Y.520, D:Y.520, D:N.621 Water bridges: D:N.119, D:D.218, D:D.218, D:D.218

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saur, M. et al., Fragment-based drug discovery using cryo-EM. Drug Discov Today (2020)

Release Date

2020-01-08

Peptides

Beta-galactosidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Beta-galactosidase

Related Entries With Identical Sequence