SMTL ID : 3vio.2 (1 other biounit)

Crystal structure of beta-glucosidase from termite Neotermes koshunensis in complex with a new glucopyranosidic product

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.12 Å

Oligo State

homo-dimer

Ligands

2 x GBE: 3-{4-[2-(beta-D-glucopyranosyloxy)ethyl]piperazin-1-yl}propane-1-sulfonic acid(Non-covalent)

GBE.1: 15 residues within 4Å: Chain A: Q.26, H.129, W.130, N.173, D.174, T.177, N.234, Y.318, S.354, W.355, E.383, W.425, E.432, W.433, F.441 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Q.26, A:Q.26, A:H.129, A:N.173, A:D.174 Water bridges: A:D.174, A:N.316, A:S.353, A:S.353, A:S.354, A:S.354, A:N.430 GBE.5: 15 residues within 4Å: Chain B: Q.26, H.129, W.130, N.173, D.174, T.177, N.234, Y.318, S.354, W.355, E.383, W.425, E.432, W.433, F.441 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:Q.26, B:Q.26, B:H.129, B:N.173 Water bridges: B:D.174, B:N.316, B:S.353, B:S.353, B:S.354, B:S.354, B:N.430

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: N.284, D.287, E.288, E.331, R.336 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.288, A:E.331, A:E.331, A:R.336 GOL.6: 5 residues within 4Å: Chain B: N.284, D.287, E.288, E.331, R.336 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.331, B:R.336

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 2 residues within 4Å: Chain A: K.160, N.161 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.160, A:K.160, A:N.161 NA.7: 2 residues within 4Å: Chain B: K.160, N.161 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.160, B:K.160, B:N.161

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

CL.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jeng, W.Y. et al., High-resolution structures of Neotermes koshunensis beta-glucosidase mutants provide insights into the catalytic mechanism and the synthesis of glucoconjugates. Acta Crystallogr.,Sect.D (2012)

Release Date

2012-07-04

Peptides

Beta-glucosidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Beta-glucosidase

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