SMTL ID : 8i5s.1

Crystal structure of TxGH116 D593N acid/base mutant from Thermoanaerobacterium xylanolyticum with 2-deoxy-2-fluoroglucoside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

1 x G2F: 2-deoxy-2-fluoro-alpha-D-glucopyranose(Post Translational Modification)

G2F.1: 15 residues within 4Å: Chain A: E.426, Y.430, T.435, D.437, V.438, H.492, W.516, T.576, N.578, W.717, E.762, R.771, Y.775, R.777 Ligands: GOL.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.437, A:H.492, A:R.771, A:R.771, A:R.777

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: R.417, T.418, N.419 Ligands: GOL.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.417, A:T.418, A:N.419, A:N.419 GOL.3: 5 residues within 4Å: Chain A: Y.430, Y.432, Y.508, W.510 Ligands: GOL.4 No protein-ligand interaction detected (PLIP) GOL.4: 8 residues within 4Å: Chain A: Y.47, Y.430, N.578, T.579, Q.712, R.771 Ligands: G2F.1, GOL.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.430, A:N.578, A:Q.712 Water bridges: A:T.579 GOL.5: 4 residues within 4Å: Chain A: I.50, F.428, D.429, 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.6: 4 residues within 4Å: Chain A: K.160, K.181, E.368, D.372 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.181, A:K.181, A:D.372 Water bridges: A:D.23, A:D.372, A:D.372 GOL.7: 4 residues within 4Å: Chain A: G.347, K.348, N.349, N.352 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.348, A:N.349, A:N.349, A:N.352 Water bridges: A:T.343 GOL.8: 8 residues within 4Å: Chain A: W.580, S.581, F.639, S.643, D.644, H.645, D.707, S.709 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.581, A:S.643, A:H.645, A:H.645, A:D.707, A:S.709 Water bridges: A:S.581, A:D.644 GOL.9: 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.10: 2 residues within 4Å: Chain A: T.551, D.554 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.551 Water bridges: A:K.550 GOL.11: 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:T.90 GOL.12: 8 residues within 4Å: Chain A: N.419, Q.456, R.459, Q.460, D.463, Y.544 Ligands: GOL.2, NFG.17 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.456, A:R.459, A:R.459, A:D.463 GOL.13: 5 residues within 4Å: Chain A: I.166, P.167, Y.168, N.169, M.370 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.168, A:N.169 Water bridges: A:N.169 GOL.14: 8 residues within 4Å: Chain A: V.467, D.469, K.484, K.485, I.503, K.504, I.505 Ligands: NFG.17 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.469, A:I.503, A:K.504, A:K.504, A:I.505

1 x CA: CALCIUM ION(Non-covalent)

CA.15: 5 residues within 4Å: Chain A: D.560, D.562, D.564, I.566, D.568 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.560, A:D.562, A:D.564, A:I.566, A:D.568

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

EDO.16: 9 residues within 4Å: Chain A: G.66, T.67, H.80, I.83, A.400, D.401, G.402, G.403, T.404 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.80, A:G.84, A:D.401, A:G.403, A:T.404

2 x NFG: 2,4-dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucopyranoside(Non-covalent)

NFG.17: 11 residues within 4Å: Chain A: M.421, Q.460, D.463, T.464, V.467, L.494, W.502, I.503, I.505 Ligands: GOL.12, GOL.14 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.463, A:T.464, A:I.505 NFG.18: 6 residues within 4Å: Chain A: V.269, G.272, D.273, S.275, D.276, H.279 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.273 Water bridges: A:V.269, A:G.272

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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