SMTL ID : 5bvu.1

Crystal structure of Thermoanaerobacterium xylolyticum GH116 beta-glucosidase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

monomer

Ligands

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 12 residues within 4Å: Chain A: E.426, Y.430, T.435, D.437, H.492, W.516, T.576, D.578, E.762, Y.775, R.777 Ligands: GOL.2 Ligand excluded by PLIP GOL.2: 8 residues within 4Å: Chain A: Y.430, Y.432, Y.508, W.510, D.578, Q.712, R.771 Ligands: GOL.1 Ligand excluded by PLIP GOL.3: 4 residues within 4Å: Chain A: I.50, F.428, D.429, Y.498 Ligand excluded by PLIP GOL.4: 4 residues within 4Å: Chain A: K.160, K.181, E.368, D.372 Ligand excluded by PLIP GOL.5: 3 residues within 4Å: Chain A: G.347, K.348, N.349 Ligand excluded by PLIP GOL.6: 8 residues within 4Å: Chain A: W.580, S.581, F.639, S.643, D.644, H.645, D.707, S.709 Ligand excluded by PLIP GOL.7: 7 residues within 4Å: Chain A: Y.170, W.406, N.419, N.420, D.452, I.453, Q.456 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: K.547, K.550, T.551, D.554 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: Y.88, T.89, T.90, Y.92, Y.114 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain A: I.222, K.223, D.224, F.354, K.358 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain A: K.223, E.230, V.232, I.262, Y.264, N.289 Ligand excluded by PLIP 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.17 Ligand excluded by PLIP GOL.13: 7 residues within 4Å: Chain A: N.419, M.421, Q.456, R.459, Q.460, D.463, Y.544 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain A: I.378, M.448, L.449, W.782, E.785 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain A: I.166, P.167, Y.168, N.169, M.370 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain A: V.467, D.469, I.503, K.504, I.505 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.17: 6 residues within 4Å: Chain A: D.560, D.562, D.564, I.566, D.568 Ligands: GOL.12 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.3

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

EDO.18: 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:G.84, A:D.401, A:G.403, A:T.404 Water bridges: A:G.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Charoenwattanasatien, R. et al., Bacterial beta-Glucosidase Reveals the Structural and Functional Basis of Genetic Defects in Human Glucocerebrosidase 2 (GBA2). Acs Chem.Biol. (2016)

Release Date

2016-05-18

Peptides

beta-glucosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

beta-glucosidase

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