- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.50 Å
- Oligo State
- monomer
- Ligands
- 1 x BGC- BGC: beta-D-glucopyranose-(1-4)-beta-D-glucopyranose(Non-covalent)
- 14 x GOL: GLYCEROL(Non-functional Binders)
GOL.2: 5 residues within 4Å:- Chain A: I.50, F.428, D.429, Y.498
- Ligands: EDO.17
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:F.428, A:Y.498
- Water bridges: A:N.431
GOL.3: 4 residues within 4Å:- Chain A: K.160, K.181, E.368, D.372
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:K.181, A:K.181, A:D.372
- Water bridges: A:D.372
GOL.4: 3 residues within 4Å:- Chain A: G.347, K.348, N.349
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:K.348, A:N.349, A:N.352
- Water bridges: A:F.346, A:N.352
GOL.5: 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.6: 9 residues within 4Å:- Chain A: W.29, T.30, I.31, E.35, F.37, Y.749, D.750, K.751, W.757
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:Y.749
- Water bridges: A:T.30, A:E.35, A:K.751, A:K.751
GOL.7: 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.8: 5 residues within 4Å:- Chain A: V.467, D.469, 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, A:I.505
- Water bridges: A:D.469
GOL.9: 4 residues within 4Å:- Chain A: K.547, K.550, T.551, D.554
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:T.551
GOL.10: 4 residues within 4Å:- Chain A: R.417, T.418, N.419
- Ligands: GOL.13
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.417, A:T.418, A:N.419
GOL.11: 5 residues within 4Å:- Chain A: Y.88, T.89, T.90, Y.92, Y.114
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:T.89, A:T.90, A:T.90, A:Y.92
- Water bridges: A:Y.88, A:T.90
GOL.12: 9 residues within 4Å:- Chain A: D.562, D.564, D.568, G.584, T.585, E.630, T.641, E.642
- Ligands: CA.15
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:D.568, A:E.630, A:T.641
GOL.13: 8 residues within 4Å:- Chain A: N.419, M.421, Q.456, R.459, Q.460, D.463, Y.544
- Ligands: GOL.10
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:Q.456, A:R.459, A:R.459
- Water bridges: A:D.463, A:D.463
GOL.14: 5 residues within 4Å:- Chain A: I.166, P.167, Y.168, N.169, M.370
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.169
GOL.18: 4 residues within 4Å:- Chain A: V.45, K.46, Y.47
- Ligands: BGC-BGC.1
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:K.46, A:Y.47, A:Y.47
- 1 x CA: CALCIUM ION(Non-covalent)
- 2 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
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:H.80, A:D.401, A:G.403, A:T.404
- Water bridges: A:G.66, A:G.84
EDO.17: 6 residues within 4Å:- Chain A: D.429, Y.430, N.431, Y.432
- Ligands: BGC-BGC.1, GOL.2
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:N.431
- Water bridges: A:D.429, A:N.431, A:S.496
- 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
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.50 Å
- Oligo State
- monomer
- Ligands
- 1 x BGC- BGC: beta-D-glucopyranose-(1-4)-beta-D-glucopyranose(Non-covalent)
- 14 x GOL: GLYCEROL(Non-functional Binders)
- 1 x CA: CALCIUM ION(Non-covalent)
- 2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 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