SMTL ID : 5a1a.1

2.2 A resolution cryo-EM structure of beta-galactosidase in complex with a cell-permeant inhibitor

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x PTQ: 2-phenylethyl 1-thio-beta-D-galactopyranoside(Non-covalent)

PTQ.1: 12 residues within 4Å: Chain A: N.101, D.200, E.460, M.501, Y.502, E.536, H.539, D.597, F.600, V.794, W.998 Ligands: NA.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:N.101, A:F.600, A:V.794, A:W.998 Hydrogen bonds: A:N.101, A:E.460, A:E.536, A:F.600 Water bridges: A:E.536 pi-Stacking: A:F.600 PTQ.6: 12 residues within 4Å: Chain B: N.101, D.200, E.460, M.501, Y.502, E.536, H.539, D.597, F.600, V.794, W.998 Ligands: NA.9 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:N.101, B:F.600, B:V.794, B:W.998 Hydrogen bonds: B:N.101, B:E.460, B:E.536, B:F.600 Water bridges: B:E.536 pi-Stacking: B:F.600 PTQ.11: 12 residues within 4Å: Chain C: N.101, D.200, E.460, M.501, Y.502, E.536, H.539, D.597, F.600, V.794, W.998 Ligands: NA.14 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:N.101, C:F.600, C:V.794, C:W.998 Hydrogen bonds: C:N.101, C:D.200, C:E.460, C:Y.502, C:F.600 Water bridges: C:E.536 pi-Stacking: C:F.600 PTQ.16: 12 residues within 4Å: Chain D: N.101, D.200, E.460, M.501, Y.502, E.536, H.539, D.597, F.600, V.794, W.998 Ligands: NA.19 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:N.101, D:F.600, D:V.794, D:W.998 Hydrogen bonds: D:N.101, D:D.200, D:E.460, D:Y.502, D:F.600 Water bridges: D:E.536 pi-Stacking: D:F.600

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.415, H.417, E.460 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.415, A:H.417, H2O.2, H2O.2, H2O.3 MG.3: 7 residues within 4Å: Chain A: D.14, W.15, N.17, V.20, Y.160, Q.162, D.192 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.14, A:N.17, A:V.20, A:D.192, A:D.192 MG.7: 3 residues within 4Å: Chain B: E.415, H.417, E.460 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.415, B:H.417, H2O.9, H2O.9, H2O.11 MG.8: 7 residues within 4Å: Chain B: D.14, W.15, N.17, V.20, Y.160, Q.162, D.192 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.14, B:N.17, B:V.20, B:D.192, B:D.192 MG.12: 3 residues within 4Å: Chain C: E.415, H.417, E.460 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.415, C:H.417, H2O.17, H2O.17, H2O.18 MG.13: 7 residues within 4Å: Chain C: D.14, W.15, N.17, V.20, Y.160, Q.162, D.192 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.14, C:N.17, C:V.20, C:D.192, C:D.192 MG.17: 3 residues within 4Å: Chain D: E.415, H.417, E.460 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.415, D:H.417, H2O.24, H2O.24, H2O.26 MG.18: 7 residues within 4Å: Chain D: D.14, W.15, N.17, V.20, Y.160, Q.162, D.192 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.14, D:N.17, D:V.20, D:D.192, D:D.192

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

NA.4: 7 residues within 4Å: Chain A: Y.99, D.200, H.539, W.567, F.600, N.603 Ligands: PTQ.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.567, A:N.603 NA.5: 4 residues within 4Å: Chain A: F.555, Y.558, P.559, L.561 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.555 NA.9: 7 residues within 4Å: Chain B: Y.99, D.200, H.539, W.567, F.600, N.603 Ligands: PTQ.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.539, B:N.603 NA.10: 4 residues within 4Å: Chain B: F.555, Y.558, P.559, L.561 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.561 NA.14: 7 residues within 4Å: Chain C: Y.99, D.200, H.539, W.567, F.600, N.603 Ligands: PTQ.11 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.539, C:N.603 NA.15: 4 residues within 4Å: Chain C: F.555, Y.558, P.559, L.561 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:F.555 NA.19: 7 residues within 4Å: Chain D: Y.99, D.200, H.539, W.567, F.600, N.603 Ligands: PTQ.16 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.539, D:N.603 NA.20: 4 residues within 4Å: Chain D: F.555, Y.558, P.559, L.561 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:P.559

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bartesaghi, A. et al., 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with a Cell-Permeant Inhibitor. Science (2015)

Release Date

2015-05-06

Peptides

BETA-GALACTOSIDASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

BETA-GALACTOSIDASE