SMTL ID : 6cvm.1

Atomic resolution cryo-EM structure of beta-galactosidase

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

PTQ.1: 17 residues within 4Å: Chain A: N.101, V.102, D.200, H.390, N.459, E.460, M.501, Y.502, E.536, H.539, W.567, D.597, F.600, N.603, V.794, W.998 Ligands: NA.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.102, A:V.794, A:W.998 Hydrogen bonds: A:N.101, A:D.200, A:H.390, A:N.459, A:Y.502, A:W.567 Water bridges: A:D.200, A:H.417 pi-Stacking: A:F.600 PTQ.6: 17 residues within 4Å: Chain B: N.101, V.102, D.200, H.390, N.459, E.460, M.501, Y.502, E.536, H.539, W.567, D.597, F.600, N.603, V.794, W.998 Ligands: NA.9 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.102, B:V.794, B:W.998 Hydrogen bonds: B:N.101, B:D.200, B:H.390, B:N.459, B:Y.502, B:W.567 Water bridges: B:D.200, B:H.417 pi-Stacking: B:F.600 PTQ.11: 17 residues within 4Å: Chain C: N.101, V.102, D.200, H.390, N.459, E.460, M.501, Y.502, E.536, H.539, W.567, D.597, F.600, N.603, V.794, W.998 Ligands: NA.14 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:V.102, C:V.794, C:W.998 Hydrogen bonds: C:N.101, C:H.390, C:N.459, C:W.567 Water bridges: C:D.200 pi-Stacking: C:F.600 PTQ.16: 17 residues within 4Å: Chain D: N.101, V.102, D.200, H.390, N.459, E.460, M.501, Y.502, E.536, H.539, W.567, D.597, F.600, N.603, V.794, W.998 Ligands: NA.19 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:V.102, D:V.794, D:W.998 Hydrogen bonds: D:N.101, D:H.390, D:N.459, D:W.567 Water bridges: D:D.200 pi-Stacking: D:F.600

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: N.101, 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.5, H2O.8 MG.3: 6 residues within 4Å: Chain A: D.14, N.17, V.20, Y.160, Q.162, D.192 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.14, A:N.17, A:V.20, A:D.192 MG.7: 4 residues within 4Å: Chain B: N.101, 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.42, H2O.46, H2O.48 MG.8: 6 residues within 4Å: Chain B: D.14, N.17, V.20, Y.160, Q.162, D.192 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.14, B:N.17, B:V.20, B:D.192 MG.12: 4 residues within 4Å: Chain C: N.101, 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.83, H2O.86, H2O.88 MG.13: 6 residues within 4Å: Chain C: D.14, N.17, V.20, Y.160, Q.162, D.192 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.14, C:N.17, C:V.20, C:D.192 MG.17: 4 residues within 4Å: Chain D: N.101, 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.123, H2O.126, H2O.128 MG.18: 6 residues within 4Å: Chain D: D.14, N.17, V.20, Y.160, Q.162, D.192 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.14, D:N.17, D:V.20, D:D.192

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

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bartesaghi, A. et al., Atomic Resolution Cryo-EM Structure of beta-Galactosidase. Structure (2018)

Release Date

2018-05-30

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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