SMTL ID : 4ucf.1

Crystal structure of Bifidobacterium bifidum beta-galactosidase in complex with alpha-galactose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-trimer

Ligands

7 x GLA: alpha-D-galactopyranose(Non-covalent)(Post Translational Modification)

GLA.1: 13 residues within 4Å: Chain A: F.56, R.122, N.160, E.161, N.262, D.287, Y.289, E.320, W.328, F.358, E.368, H.371 Ligands: GLA.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.122, A:R.122, A:N.160, A:E.161, A:N.262, A:D.287, A:Y.289, A:W.328, A:E.368 Water bridges: A:N.160, A:E.320 GLA.2: 4 residues within 4Å: Chain A: E.161, C.164, W.328 Ligands: GLA.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.161 GLA.3: 5 residues within 4Å: Chain A: R.19, G.47, N.49, G.396, S.399 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.19, A:R.19, A:N.49, A:S.399 Water bridges: A:G.396 Salt bridges: A:K.44 GLA.4: 13 residues within 4Å: Chain B: F.56, R.122, N.160, E.161, N.262, D.287, Y.289, E.320, W.328, F.358, E.368, H.371 Ligands: GLA.5 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.122, B:R.122, B:N.160, B:E.161, B:N.262, B:D.287, B:Y.289, B:W.328, B:E.368 Water bridges: B:N.160, B:E.320 GLA.5: 3 residues within 4Å: Chain B: E.161, W.328 Ligands: GLA.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.161, B:W.328 Water bridges: B:R.122 GLA.6: 13 residues within 4Å: Chain C: F.56, R.122, N.160, E.161, N.262, D.287, Y.289, E.320, W.328, F.358, E.368, H.371 Ligands: GLA.7 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:R.122, C:R.122, C:N.160, C:E.161, C:N.262, C:Y.289, C:W.328, C:E.368 Water bridges: C:N.160, C:E.320 GLA.7: 4 residues within 4Å: Chain C: E.161, C.164, W.328 Ligands: GLA.6 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.161 Water bridges: C:R.122, C:R.122, C:S.266, C:D.287

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 4 residues within 4Å: Chain C: H.104, E.134, Y.135, N.138 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.104, C:N.138

1 x POL: N-PROPANOL(Non-covalent)

POL.9: 3 residues within 4Å: Chain C: Q.102, A.103, P.105 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Godoy, A.S. et al., Crystal Structure of Beta1-6-Galactosidase from Bifidobacterium Bifidum S17: Trimeric Architecture, Molecular Determinants of the Enzymatic Activity and its Inhibition by Alpha-Galactose. FEBS J. (2016)

Release Date

2016-01-20

Peptides

BETA-GALACTOSIDASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

BETA-GALACTOSIDASE

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