SMTL ID : 7ms2.1

Three-dimensional structure of a GH3 Beta-glucosidase from Clostridium thermocellum in complex with glycerol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-dimer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: W.27, D.44, R.50, L.105, D.231, W.232, S.351, E.420 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.50, A:D.231, A:S.351, A:E.420 Water bridges: A:R.119, A:Y.199 GOL.2: 4 residues within 4Å: Chain A: Y.532, K.536 Chain B: Y.532, K.536 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.532, B:K.536, B:K.536, A:K.536 Water bridges: B:P.508, A:K.536 GOL.3: 7 residues within 4Å: Chain A: H.161, R.162, G.421, F.422 Chain B: E.685, A.721, N.725 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.160, A:R.162, A:D.423, B:N.725, B:N.725 GOL.6: 8 residues within 4Å: Chain B: W.27, D.44, R.50, L.105, D.231, W.232, S.351, E.420 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.50, B:E.420 Water bridges: B:Y.199 GOL.7: 2 residues within 4Å: Chain B: S.735, Q.736 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.736, B:Q.736

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.4: 6 residues within 4Å: Chain A: Y.129, S.132, A.181, E.184, N.185, R.630 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.132, A:A.181, A:N.185 Water bridges: A:N.185 BME.8: 6 residues within 4Å: Chain B: Y.129, S.132, A.181, E.184, N.185, R.630 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.132, B:A.181, B:N.185

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 6 residues within 4Å: Chain A: N.110, I.111, A.156, N.158, Y.179, F.183 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain B: N.110, I.111, A.156, N.158, Y.179, F.183 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Almeida, L.R. et al., Three-dimensional structure of a GH3 Beta-glucosidase from Clostridium thermocellum in complex with glycerol. To Be Published

Release Date

2022-05-18

Peptides

Thermostable beta-glucosidase B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thermostable beta-glucosidase B