SMTL ID : 5xxm.1

Crystal structure of GH3 beta-glucosidase from Bacteroides thetaiotaomicron in complex with gluconolactone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.680, V.682, P.730 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.680, A:V.682, H2O.1, H2O.2, H2O.2, H2O.8 MG.4: 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.30, H2O.30, H2O.30, H2O.30

2 x LGC: D-glucono-1,5-lactone(Non-covalent)

LGC.2: 13 residues within 4Å: Chain A: T.40, F.61, D.91, F.135, R.149, K.188, H.189, M.232, F.235, D.267, Y.268, M.298, E.504 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.40, A:R.149, A:R.149, A:K.188, A:H.189, A:E.504 Water bridges: A:K.188, B:R.603 LGC.5: 13 residues within 4Å: Chain B: T.40, F.61, D.91, F.135, R.149, K.188, H.189, M.232, F.235, D.267, Y.268, M.298, E.504 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.149, B:R.149, B:K.188, B:H.189, B:E.504 Water bridges: B:K.188, A:R.603

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

PG4.3: 5 residues within 4Å: Chain A: F.13, A.16, L.17, K.20, L.82 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.20, A:L.82

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

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