SMTL ID : 6x1q.1

1.8 Angstrom resolution structure of b-galactosidase with a 200 kV cryoARM electron microscope

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: V.102, D.200, E.415, H.417, N.459, E.460 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.415, A:H.417, A:E.460, H2O.1, H2O.5, H2O.6 MG.2: 9 residues within 4Å: Chain A: D.14, W.15, N.17, P.18, V.20, T.21, 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.5: 6 residues within 4Å: Chain B: V.102, D.200, E.415, H.417, N.459, E.460 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.415, B:H.417, B:E.460, H2O.36, H2O.40, H2O.40 MG.6: 9 residues within 4Å: Chain B: D.14, W.15, N.17, P.18, V.20, T.21, 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.9: 6 residues within 4Å: Chain C: V.102, D.200, E.415, H.417, N.459, E.460 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.415, C:H.417, C:E.460, H2O.71, H2O.75, H2O.75 MG.10: 9 residues within 4Å: Chain C: D.14, W.15, N.17, P.18, V.20, T.21, 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.13: 6 residues within 4Å: Chain D: V.102, D.200, E.415, H.417, N.459, E.460 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.415, D:H.417, D:E.460, H2O.106, H2O.109, H2O.110 MG.14: 9 residues within 4Å: Chain D: D.14, W.15, N.17, P.18, V.20, T.21, 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.3: 7 residues within 4Å: Chain A: Y.99, D.200, H.539, W.567, F.600, C.601, N.603 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.99, A:W.567, A:N.603, A:N.603 Water bridges: A:D.200 NA.4: 6 residues within 4Å: Chain A: L.349, F.555, Y.558, P.559, L.561, Q.562 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.559, A:L.561 NA.7: 7 residues within 4Å: Chain B: Y.99, D.200, H.539, W.567, F.600, C.601, N.603 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.99, B:D.200, B:W.567, B:N.603 NA.8: 6 residues within 4Å: Chain B: L.349, F.555, Y.558, P.559, L.561, Q.562 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.555, B:L.561 NA.11: 7 residues within 4Å: Chain C: Y.99, D.200, H.539, W.567, F.600, C.601, N.603 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.99, C:Y.99, C:W.567, C:N.603 NA.12: 6 residues within 4Å: Chain C: L.349, F.555, Y.558, P.559, L.561, Q.562 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:P.559, C:L.561 NA.15: 7 residues within 4Å: Chain D: Y.99, D.200, H.539, W.567, F.600, C.601, N.603 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.99, D:W.567, D:F.600, D:N.603 NA.16: 6 residues within 4Å: Chain D: L.349, F.555, Y.558, P.559, L.561, Q.562 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:F.555, D:L.561

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Merk, A. et al., 1.8 angstrom resolution structure of beta-galactosidase with a 200 kV CRYO ARM electron microscope. Iucrj (2020)

Release Date

2020-07-01

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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