SMTL ID : 3oba.1

Structure of the beta-galactosidase from Kluyveromyces lactis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-tetramer

Ligands

4 x MN3: MANGANESE (III) ION(Covalent)

MN3.1: 4 residues within 4Å: Chain A: D.600, A.981, H.982, D.985 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.600, A:H.982, A:D.985, A:D.985 MN3.4: 5 residues within 4Å: Chain B: D.600, V.601, A.981, H.982, D.985 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.600, B:D.600, B:H.982, B:D.985, B:D.985 MN3.9: 4 residues within 4Å: Chain C: D.600, A.981, H.982, D.985 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.600, C:D.600, C:H.982, C:D.985, C:D.985 MN3.12: 5 residues within 4Å: Chain D: D.600, V.601, A.981, H.982, D.985 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.600, D:D.600, D:H.982, D:D.985, D:D.985

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: F.225, D.227, Y.230, Q.339, E.341, K.343 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.225, A:Q.339, A:K.343 GOL.3: 7 residues within 4Å: Chain A: K.787, W.796, R.797, P.798, R.886, E.890, R.995 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.787, A:R.886, A:R.995 GOL.5: 9 residues within 4Å: Chain B: Q.195, W.196, H.362, D.363, H.364, G.369, R.370, Y.397, H.594 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:W.196, B:G.369, B:R.370, B:Y.397, B:Y.397, B:H.594 GOL.6: 8 residues within 4Å: Chain A: L.771, F.788, G.790, K.820, Q.821, N.822 Chain B: P.108, V.110 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:V.110, A:G.790, A:N.822 GOL.7: 10 residues within 4Å: Chain B: S.569, L.570, K.571, E.572, E.645, V.649, D.913, K.914, K.915, E.916 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.569, B:K.571, B:E.645, B:P.912, B:K.915, B:E.916, B:E.916, B:E.916 GOL.8: 9 residues within 4Å: Chain A: P.108, T.109, V.110 Chain B: L.771, F.788, G.790, K.820, Q.821, N.822 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:Q.821, A:T.109 Hydrogen bonds: A:T.109, A:V.110 GOL.10: 2 residues within 4Å: Chain C: N.634, N.638 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.634, C:N.638 GOL.11: 9 residues within 4Å: Chain C: L.771, F.788, G.790, K.820, Q.821, N.822 Chain D: P.108, T.109, V.110 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:T.109, D:V.110, C:G.790, C:N.822 Water bridges: C:N.822, C:N.822 GOL.13: 7 residues within 4Å: Chain D: K.787, W.796, R.797, P.798, R.886, E.890, R.995 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.995, D:R.995 Water bridges: D:K.787, D:E.890 GOL.14: 8 residues within 4Å: Chain C: P.108, T.109, V.110 Chain D: F.788, G.790, K.820, Q.821, N.822 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:T.109, C:V.110 Water bridges: D:N.822

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pereira-Rodriguez, A. et al., Structural basis of specificity in tetrameric Kluyveromyces lactis beta-galactosidase. J.Struct.Biol. (2012)

Release Date

2011-08-17

Peptides

Beta-galactosidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
B

Beta-galactosidase

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