SMTL ID : 4ha3.1

Structure of beta-glycosidase from Acidilobus saccharovorans in complex with Tris

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

homo-tetramer

Ligands

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 12 residues within 4Å: Chain A: Q.18, H.151, W.152, N.206, E.207, Y.319, E.384, W.422, E.429, W.430, F.438 Ligands: GOL.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.18, A:N.206, A:E.207, A:Y.319, A:Y.319 TRS.8: 12 residues within 4Å: Chain B: Q.18, H.151, W.152, N.206, E.207, Y.319, E.384, W.422, E.429, W.430, F.438 Ligands: GOL.13 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.18, B:N.206, B:E.207, B:Y.319, B:Y.319 TRS.15: 12 residues within 4Å: Chain C: Q.18, H.151, W.152, N.206, E.207, Y.319, E.384, W.422, E.429, W.430, F.438 Ligands: GOL.20 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.18, C:N.206, C:E.207, C:Y.319 TRS.22: 12 residues within 4Å: Chain D: Q.18, H.151, W.152, N.206, E.207, Y.319, E.384, W.422, E.429, W.430, F.438 Ligands: GOL.27 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.18, D:N.206, D:E.207, D:Y.319

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: E.390, R.437, M.442, R.453 Chain C: P.480 Ligand excluded by PLIP GOL.3: 5 residues within 4Å: Chain A: V.111, E.113, L.116, A.253, I.254 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: G.46, L.47, V.48, S.49, S.221, A.431 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: W.152, L.214, F.223, F.356, E.429, W.430 Ligands: TRS.1 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain B: E.390, R.437, M.442, R.453 Chain D: P.480 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain B: V.111, E.113, L.116, A.253, I.254 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain B: G.46, L.47, V.48, S.49, S.221, A.431 Ligand excluded by PLIP GOL.13: 7 residues within 4Å: Chain B: W.152, L.214, F.223, F.356, E.429, W.430 Ligands: TRS.8 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain A: P.480 Chain C: E.390, R.437, M.442, R.453 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain C: V.111, E.113, L.116, A.253, I.254 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain C: G.46, L.47, V.48, S.49, S.221, A.431 Ligand excluded by PLIP GOL.20: 7 residues within 4Å: Chain C: W.152, L.214, F.223, F.356, E.429, W.430 Ligands: TRS.15 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain B: P.480 Chain D: E.390, R.437, M.442, R.453 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain D: V.111, E.113, L.116, A.253, I.254 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain D: G.46, L.47, V.48, S.49, S.221, A.431 Ligand excluded by PLIP GOL.27: 7 residues within 4Å: Chain D: W.152, L.214, F.223, F.356, E.429, W.430 Ligands: TRS.22 Ligand excluded by PLIP

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain A: D.392, Y.393 Chain C: D.392, Y.393 Ligands: MG.19 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: A:D.392, C:D.392, H2O.1, H2O.2, H2O.42 MG.12: 5 residues within 4Å: Chain B: D.392, Y.393 Chain D: D.392, Y.393 Ligands: MG.26 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: D:D.392, B:D.392, H2O.21, H2O.22, H2O.62 MG.19: 5 residues within 4Å: Chain A: D.392, Y.393 Chain C: D.392, Y.393 Ligands: MG.5 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: A:D.392, C:D.392, H2O.2, H2O.41, H2O.42 MG.26: 5 residues within 4Å: Chain B: D.392, Y.393 Chain D: D.392, Y.393 Ligands: MG.12 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: D:D.392, B:D.392, H2O.22, H2O.61, H2O.62

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 2 residues within 4Å: Chain A: R.321, A.349 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.321, A:R.321 Water bridges: A:P.270 PEG.14: 2 residues within 4Å: Chain B: R.321, A.349 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.321, B:R.321 Water bridges: B:P.270 PEG.21: 2 residues within 4Å: Chain C: R.321, A.349 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.321, C:R.321 Water bridges: C:P.270 PEG.28: 2 residues within 4Å: Chain D: R.321, A.349 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.321, D:R.321 Water bridges: D:P.270

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trofimov, A.A. et al., Structures of beta-glycosidase from Acidilobus saccharovorans in complexes with tris and glycerol. Dokl.Biochem.Biophys.

Release Date

2012-10-10

Peptides

Beta-galactosidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Beta-galactosidase

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