SMTL ID : 8ibr.1

Crystal structure of GH42 beta-galactosidase BiBga42A from Bifidobacterium longum subspecies infantis in complex with glycerol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-trimer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: F.55, R.121, N.159, E.160, N.260, D.285, E.318, F.356, E.366 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.121, A:R.121, A:N.159, A:E.160, A:N.260, A:E.366 Water bridges: A:N.159, A:E.318 GOL.3: 9 residues within 4Å: Chain B: F.55, R.121, N.159, E.160, N.260, D.285, E.318, F.356, E.366 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.121, B:R.121, B:N.159, B:E.160, B:N.260, B:E.366 Water bridges: B:N.159, B:E.318 GOL.5: 9 residues within 4Å: Chain C: F.55, R.121, N.159, E.160, N.260, D.285, E.318, F.356, E.366 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:R.121, C:R.121, C:N.159, C:E.160, C:N.260, C:E.366 Water bridges: C:N.159, C:E.318

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

PEG.2: 3 residues within 4Å: Chain A: T.127, L.132, D.240 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.127 Water bridges: A:F.241 PEG.4: 3 residues within 4Å: Chain B: T.127, L.132, D.240 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.127 Water bridges: B:F.241 PEG.6: 3 residues within 4Å: Chain C: T.127, L.132, D.240 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.127 Water bridges: C:F.241

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gotoh, A. et al., Substrate recognition mode of a glycoside hydrolase family 42 beta-galactosidase from Bifidobacterium longum subspecies infantis ( Bi Bga42A) revealed by crystallographic and mutational analyses. Microbiome Res Rep (2023)

Release Date

2023-06-07

Peptides

Beta-galactosidase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Beta-galactosidase