SMTL ID : 3ob8.1

Structure of the beta-galactosidase from Kluyveromyces lactis in complex with galactose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

4 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.1: 14 residues within 4Å: Chain A: N.95, D.194, H.396, N.488, E.489, M.529, Y.530, E.558, H.561, W.589, F.627, D.630 Ligands: MG.2, NA.7 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.194, A:H.396, A:N.488, A:E.489, A:Y.530, A:D.630 Water bridges: A:D.194 GAL.8: 14 residues within 4Å: Chain B: N.95, D.194, H.396, N.488, E.489, M.529, Y.530, E.558, H.561, W.589, F.627, D.630 Ligands: MG.9, NA.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.194, B:H.396, B:N.488, B:E.489, B:Y.530 GAL.15: 14 residues within 4Å: Chain C: N.95, D.194, H.396, N.488, E.489, M.529, Y.530, E.558, H.561, W.589, F.627, D.630 Ligands: MG.16, NA.21 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:H.396, C:N.488, C:E.489 Water bridges: C:N.95, C:D.194, C:D.194, C:H.396 GAL.22: 14 residues within 4Å: Chain D: N.95, D.194, H.396, N.488, E.489, M.529, Y.530, E.558, H.561, W.589, F.627, D.630 Ligands: MG.23, NA.28 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.488, D:E.489, D:E.489, D:E.558 Water bridges: D:D.194, D:D.194, D:H.396

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: N.95, D.194, E.421, H.423, E.489 Ligands: GAL.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.421, A:H.423, A:E.489 MG.9: 6 residues within 4Å: Chain B: N.95, D.194, E.421, H.423, E.489 Ligands: GAL.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.421, B:H.423, B:E.489 MG.16: 5 residues within 4Å: Chain C: N.95, E.421, H.423, E.489 Ligands: GAL.15 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.421, C:H.423, C:E.489, H2O.24, H2O.30 MG.23: 5 residues within 4Å: Chain D: N.95, E.421, H.423, E.489 Ligands: GAL.22 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.421, D:H.423, D:E.489, H2O.35

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

NA.3: 5 residues within 4Å: Chain A: T.94, N.95, D.192, Q.193, W.197 Ligand excluded by PLIP NA.4: 4 residues within 4Å: Chain A: F.577, E.580, K.581, Y.583 Ligand excluded by PLIP NA.5: 5 residues within 4Å: Chain A: Y.935, P.936, V.977, D.978, A.980 Ligand excluded by PLIP NA.7: 5 residues within 4Å: Chain A: Y.93, D.194, F.627, D.630 Ligands: GAL.1 Ligand excluded by PLIP NA.10: 5 residues within 4Å: Chain B: T.94, N.95, D.192, Q.193, W.197 Ligand excluded by PLIP NA.11: 3 residues within 4Å: Chain B: F.577, E.580, Y.583 Ligand excluded by PLIP NA.12: 5 residues within 4Å: Chain B: Y.935, P.936, V.977, D.978, A.980 Ligand excluded by PLIP NA.14: 5 residues within 4Å: Chain B: D.194, W.589, F.627, D.630 Ligands: GAL.8 Ligand excluded by PLIP NA.17: 5 residues within 4Å: Chain C: T.94, N.95, D.192, Q.193, W.197 Ligand excluded by PLIP NA.18: 3 residues within 4Å: Chain C: F.577, E.580, Y.583 Ligand excluded by PLIP NA.19: 5 residues within 4Å: Chain C: Y.935, P.936, V.977, D.978, A.980 Ligand excluded by PLIP NA.21: 5 residues within 4Å: Chain C: D.194, W.589, F.627, D.630 Ligands: GAL.15 Ligand excluded by PLIP NA.24: 5 residues within 4Å: Chain D: T.94, N.95, D.192, Q.193, W.197 Ligand excluded by PLIP NA.25: 4 residues within 4Å: Chain D: F.577, E.580, K.581, Y.583 Ligand excluded by PLIP NA.26: 5 residues within 4Å: Chain D: Y.935, P.936, V.977, D.978, A.980 Ligand excluded by PLIP NA.28: 5 residues within 4Å: Chain D: D.194, W.589, F.627, D.630 Ligands: GAL.22 Ligand excluded by PLIP

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.6: 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 MN.13: 4 residues within 4Å: Chain B: D.600, 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 MN.20: 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 MN.27: 4 residues within 4Å: Chain D: D.600, A.981, H.982, D.985 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.600, D:H.982, D:D.985, D:D.985, H2O.36

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
B

C
D

D
C

Beta-galactosidase

Related Entries With Identical Sequence