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

Crystal structure of beta-glucosidase from termite Neotermes koshunensis in complex with salicin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.15 Å

Oligo State

homo-dimer

Ligands

2 x SA0: 2-(hydroxymethyl)phenyl beta-D-glucopyranoside(Non-covalent)

SA0.1: 15 residues within 4Å: Chain A: Q.26, H.129, W.130, N.173, S.174, T.177, N.234, N.236, Y.318, W.355, E.383, W.425, E.432, W.433, F.441 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:N.234, A:Y.318, A:Y.318, A:W.355 Hydrogen bonds: A:Q.26, A:Q.26, A:H.129, A:N.173, A:S.174, A:S.174 Water bridges: A:S.353, A:S.353, A:N.430, A:E.432 SA0.7: 15 residues within 4Å: Chain B: Q.26, H.129, W.130, N.173, S.174, T.177, N.234, N.236, Y.318, W.355, E.383, W.425, E.432, W.433, F.441 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:N.234, B:Y.318, B:Y.318, B:W.355 Hydrogen bonds: B:Q.26, B:Q.26, B:H.129, B:N.173, B:S.174, B:S.174 Water bridges: B:S.353, B:N.430, B:E.432, B:E.432, B:E.432

2 x SA9: 2-(hydroxymethyl)phenol(Non-covalent)

SA9.2: 4 residues within 4Å: Chain A: E.328, G.329, Y.330, Y.335 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.330 Hydrogen bonds: A:E.328 SA9.8: 4 residues within 4Å: Chain B: E.328, G.329, Y.330, Y.335 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.330 Hydrogen bonds: B:E.328

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: S.351, A.352, S.353, S.354, K.357, Y.389 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.351, A:K.357 EDO.9: 6 residues within 4Å: Chain B: S.351, A.352, S.353, S.354, K.357, Y.389 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.351, B:K.357

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

NA.4: 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.10: 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

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

CL.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: T.242, N.243 Ligand excluded by PLIP CL.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: T.242, N.243 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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