SMTL ID : 5xxo.1

Crystal structure of mutant (D286N) GH3 beta-glucosidase from Bacteroides thetaiotaomicron in complex with sophorotriose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-dimer

Ligands

1 x BGC- BGC- BGC: beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose

BGC-BGC-BGC.1: 17 residues within 4Å: Chain A: R.603, F.614 Chain B: F.61, N.62, D.91, F.135, R.149, K.188, H.189, M.232, F.235, N.267, Y.268, M.298, W.416, V.418, E.504 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.62, B:R.149, B:R.149, B:K.188, B:H.189, B:N.267 Water bridges: B:K.188

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.680, V.682 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.680, A:V.682, H2O.1, H2O.3, H2O.4, H2O.8 MG.6: 2 residues within 4Å: Chain B: D.680, V.682 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.680, B:V.682, H2O.16, H2O.17, H2O.18, H2O.21

1 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.3: 14 residues within 4Å: Chain A: T.40, F.61, N.62, D.91, F.135, R.149, K.188, H.189, M.232, F.235, N.267, M.298, W.416, E.504 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.40, A:N.62, A:R.149, A:R.149, A:K.188, A:H.189, A:N.267, A:E.504 Water bridges: A:D.91, A:E.152

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

PEG.4: 1 residues within 4Å: Chain A: R.352 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.352 Water bridges: A:D.353

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 5 residues within 4Å: Chain A: F.13, A.16, L.17, K.20, L.82 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ishiguro, R. et al., Function and structure relationships of a beta-1,2-glucooligosaccharide-degrading beta-glucosidase. FEBS Lett. (2017)

Release Date

2017-12-13

Peptides

Periplasmic beta-glucosidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Periplasmic beta-glucosidase

Related Entries With Identical Sequence