SMTL ID : 8i5r.1

Crystal structure of TxGH116 D593N acid/base mutant from Thermoanaerobacterium xylanolyticum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: R.417, T.418, N.419 Ligands: GOL.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.417, A:T.418, A:N.419, A:N.419 GOL.2: 7 residues within 4Å: Chain A: E.426, Y.430, W.717, E.762, R.771, Y.775, R.777 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.426, A:R.771, A:R.771, A:Y.775, A:R.777 Water bridges: A:E.426, A:E.426 GOL.3: 5 residues within 4Å: Chain A: I.50, F.428, D.429, N.431, Y.498 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.428, A:Y.498 Water bridges: A:N.431, A:N.431 GOL.4: 4 residues within 4Å: Chain A: K.160, K.181, E.368, D.372 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.181, A:K.181, A:D.372 Water bridges: A:D.23, A:D.372 GOL.5: 4 residues within 4Å: Chain A: G.347, K.348, N.349, N.352 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.348, A:N.349, A:N.352 GOL.6: 7 residues within 4Å: Chain A: Y.170, W.406, N.419, N.420, D.452, I.453, Q.456 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.406, A:N.419, A:N.420 GOL.7: 4 residues within 4Å: Chain A: K.547, K.550, T.551, D.554 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.547, A:T.551 GOL.8: 5 residues within 4Å: Chain A: Y.88, T.89, T.90, Y.92, Y.114 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.89, A:T.90, A:T.90, A:Y.92 Water bridges: A:Y.88 GOL.9: 8 residues within 4Å: Chain A: N.419, M.421, Q.456, R.459, Q.460, D.463, Y.544 Ligands: GOL.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.456, A:R.459, A:R.459, A:R.459 Water bridges: A:D.463 GOL.10: 5 residues within 4Å: Chain A: I.166, P.167, Y.168, N.169, M.370 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.167, A:N.169 GOL.11: 6 residues within 4Å: Chain A: V.467, D.469, K.484, I.503, K.504, I.505 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.469, A:I.503, A:K.504, A:I.505 Water bridges: A:K.484, A:N.506

1 x CA: CALCIUM ION(Non-covalent)

CA.12: 5 residues within 4Å: Chain A: D.560, D.562, D.564, I.566, D.568 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.560, A:D.562, A:D.564, A:I.566, A:D.568, H2O.2

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

EDO.13: 9 residues within 4Å: Chain A: G.66, T.67, H.80, I.83, A.400, D.401, G.402, G.403, T.404 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.80, A:G.84, A:D.401, A:G.403

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pengthaisong, S. et al., Reaction Mechanism of Glycoside Hydrolase Family 116 Utilizes Perpendicular Protonation. Acs Catalysis (2023)

Release Date

2023-05-03

Peptides

beta-glucosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

beta-glucosidase

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