SMTL ID : 4uzs.1

Crystal structure of Bifidobacterium bifidum beta-galactosidase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-trimer

Ligands

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

PEG.1: 4 residues within 4Å: Chain A: H.104, E.134, Y.135, N.138 No protein-ligand interaction detected (PLIP) PEG.4: 1 residues within 4Å: Chain A: D.69 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.69

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: F.56, R.122, N.160, E.161, N.262, D.287, E.320, F.358, E.368 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.122, A:R.122, A:N.160, A:E.161, A:N.262, A:E.368 Water bridges: A:N.160, A:E.320, A:E.368 GOL.3: 1 residues within 4Å: Chain A: W.328 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.122, A:R.122, A:H.165, A:N.327, A:W.328 GOL.9: 7 residues within 4Å: Chain A: E.112, R.113, G.114, Y.170, S.171, R.215 Chain C: W.118 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.112, A:R.215 GOL.10: 5 residues within 4Å: Chain B: R.122, C.164, H.165, W.328 Ligands: GOL.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.122, B:H.165 Water bridges: B:N.327, B:E.368 GOL.11: 10 residues within 4Å: Chain B: F.56, R.122, N.160, E.161, N.262, D.287, E.320, F.358, E.368 Ligands: GOL.13 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.122, B:R.122, B:N.160, B:E.161, B:N.262, B:E.368 Water bridges: B:N.160, B:E.320 GOL.13: 9 residues within 4Å: Chain B: R.122, E.161, C.164, M.264, D.287, Y.289, W.328 Ligands: GOL.10, GOL.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.122, B:D.287 GOL.14: 3 residues within 4Å: Chain B: R.606, R.651, T.652 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.606, B:R.651 Water bridges: B:R.606, B:R.651, B:H.653 GOL.15: 10 residues within 4Å: Chain C: F.56, R.122, N.160, E.161, N.262, D.287, E.320, F.358, E.368 Ligands: GOL.16 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:R.122, C:R.122, C:N.160, C:E.161, C:N.262, C:E.368 Water bridges: C:E.368, C:E.368 GOL.16: 5 residues within 4Å: Chain C: R.122, E.161, C.164, M.264 Ligands: GOL.15 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.122, C:E.161

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.5: 8 residues within 4Å: Chain A: D.74, R.75, H.146, Y.147, K.148, G.149, N.150 Ligands: POL.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.71, A:N.150 Water bridges: A:G.149

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

POL.6: 6 residues within 4Å: Chain A: D.74, I.77, D.78, N.150, Y.152 Ligands: P6G.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.152, A:Y.152 Hydrogen bonds: A:D.74, A:D.78, A:N.150 POL.7: 8 residues within 4Å: Chain A: R.521, D.522, G.525, V.526, R.527, S.562, T.563, A.564 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.527 Hydrogen bonds: A:R.521, A:D.522 POL.8: 5 residues within 4Å: Chain A: L.669, A.670, H.671, T.678, D.680 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.678 Hydrogen bonds: A:A.670 POL.12: 5 residues within 4Å: Chain B: D.74, H.146, Y.147, K.148, N.150 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:D.74, B:Y.147, B:Y.147 Hydrogen bonds: B:K.148, B:N.150 POL.17: 3 residues within 4Å: Chain B: K.364 Chain C: D.506, I.511 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Water bridges: C:D.506 Hydrophobic interactions: B:K.364

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 Alpah-Galactose. FEBS J. (2016)

Release Date

2015-09-30

Peptides

BETA-GALACTOSIDASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

BETA-GALACTOSIDASE

Related Entries With Identical Sequence