SMTL ID : 4ha4.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

homo-tetramer

Ligands

4 x NA: SODIUM ION(Non-functional Binders)

NA.1: 3 residues within 4Å: Chain A: D.392 Chain C: D.392 Ligands: NA.27 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.392 NA.14: 3 residues within 4Å: Chain B: D.392 Chain D: D.392 Ligands: NA.40 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.392 NA.27: 3 residues within 4Å: Chain A: D.392 Chain C: D.392 Ligands: NA.1 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.392 NA.40: 3 residues within 4Å: Chain B: D.392 Chain D: D.392 Ligands: NA.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.392

4 x SIN: SUCCINIC ACID(Non-covalent)

SIN.2: 5 residues within 4Å: Chain A: R.460, K.464 Chain C: R.460, K.464 Ligands: SIN.28 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Water bridges: C:R.460, C:K.464, A:K.464 Salt bridges: C:R.460, C:K.464, A:R.460, A:K.464 SIN.15: 5 residues within 4Å: Chain B: R.460, K.464 Chain D: R.460, K.464 Ligands: SIN.41 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain B Water bridges: D:R.460, D:K.464, B:K.464 Salt bridges: D:R.460, D:K.464, B:R.460, B:K.464 SIN.28: 5 residues within 4Å: Chain A: R.460, K.464 Chain C: R.460, K.464 Ligands: SIN.2 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain A Water bridges: C:K.464, A:R.460, A:K.464 Salt bridges: C:R.460, C:K.464, A:R.460, A:K.464 SIN.41: 5 residues within 4Å: Chain B: R.460, K.464 Chain D: R.460, K.464 Ligands: SIN.15 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain B Water bridges: D:K.464, B:R.460, B:K.464 Salt bridges: D:R.460, D:K.464, B:R.460, B:K.464

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: W.152, L.214, F.223, F.356, E.429, W.430 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.207, A:E.429, A:A.431 GOL.4: 4 residues within 4Å: Chain A: E.390, R.437, M.442, R.453 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.390, A:R.453 Water bridges: A:R.437, A:R.437 GOL.5: 11 residues within 4Å: Chain A: Q.18, H.151, W.152, N.206, E.207, N.317, E.384, W.422, E.429, W.430 Ligands: GOL.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.18, A:Q.18, A:N.206, A:E.207, A:N.317, A:E.429 GOL.16: 7 residues within 4Å: Chain B: W.152, L.214, F.223, F.356, E.429, W.430 Ligands: GOL.18 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.207, B:E.429, B:A.431 GOL.17: 4 residues within 4Å: Chain B: E.390, R.437, M.442, R.453 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.390, B:R.453 Water bridges: B:R.437, B:R.437 GOL.18: 11 residues within 4Å: Chain B: Q.18, H.151, W.152, N.206, E.207, N.317, E.384, W.422, E.429, W.430 Ligands: GOL.16 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.18, B:Q.18, B:N.206, B:E.207, B:N.317, B:E.429 GOL.29: 7 residues within 4Å: Chain C: W.152, L.214, F.223, F.356, E.429, W.430 Ligands: GOL.31 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.429 Water bridges: C:E.207, C:E.429, C:A.431 GOL.30: 4 residues within 4Å: Chain C: E.390, R.437, M.442, R.453 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.390, C:E.390, C:R.453 Water bridges: C:R.437, C:R.437 GOL.31: 11 residues within 4Å: Chain C: Q.18, H.151, W.152, N.206, E.207, N.317, E.384, W.422, E.429, W.430 Ligands: GOL.29 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.18, C:Q.18, C:N.206, C:E.207, C:N.317, C:E.429 GOL.42: 7 residues within 4Å: Chain D: W.152, L.214, F.223, F.356, E.429, W.430 Ligands: GOL.44 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.429 Water bridges: D:E.207, D:E.429, D:A.431 GOL.43: 4 residues within 4Å: Chain D: E.390, R.437, M.442, R.453 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.390, D:E.390, D:R.453 Water bridges: D:R.437, D:R.437 GOL.44: 11 residues within 4Å: Chain D: Q.18, H.151, W.152, N.206, E.207, N.317, E.384, W.422, E.429, W.430 Ligands: GOL.42 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Q.18, D:Q.18, D:N.206, D:E.207, D:N.317, D:E.429

28 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6: 7 residues within 4Å: Chain A: N.209, V.210, G.213, L.214, Q.322, H.339 Ligands: PG4.7 Ligand excluded by PLIP PG4.7: 5 residues within 4Å: Chain A: A.264, N.265, S.266, H.339 Ligands: PG4.6 Ligand excluded by PLIP PG4.8: 5 residues within 4Å: Chain A: W.373, H.377, L.378, P.379, N.415 Ligand excluded by PLIP PG4.9: 5 residues within 4Å: Chain A: N.62, K.65, K.448, R.449, L.450 Ligand excluded by PLIP PG4.11: 5 residues within 4Å: Chain A: K.252, A.253, I.254, T.255, K.256 Ligand excluded by PLIP PG4.12: 2 residues within 4Å: Chain A: W.193, K.194 Ligand excluded by PLIP PG4.13: 5 residues within 4Å: Chain A: V.111, E.113, L.116, A.253, I.254 Ligand excluded by PLIP PG4.19: 7 residues within 4Å: Chain B: N.209, V.210, G.213, L.214, Q.322, H.339 Ligands: PG4.20 Ligand excluded by PLIP PG4.20: 5 residues within 4Å: Chain B: A.264, N.265, S.266, H.339 Ligands: PG4.19 Ligand excluded by PLIP PG4.21: 5 residues within 4Å: Chain B: W.373, H.377, L.378, P.379, N.415 Ligand excluded by PLIP PG4.22: 5 residues within 4Å: Chain B: N.62, K.65, K.448, R.449, L.450 Ligand excluded by PLIP PG4.24: 5 residues within 4Å: Chain B: K.252, A.253, I.254, T.255, K.256 Ligand excluded by PLIP PG4.25: 2 residues within 4Å: Chain B: W.193, K.194 Ligand excluded by PLIP PG4.26: 5 residues within 4Å: Chain B: V.111, E.113, L.116, A.253, I.254 Ligand excluded by PLIP PG4.32: 7 residues within 4Å: Chain C: N.209, V.210, G.213, L.214, Q.322, H.339 Ligands: PG4.33 Ligand excluded by PLIP PG4.33: 5 residues within 4Å: Chain C: A.264, N.265, S.266, H.339 Ligands: PG4.32 Ligand excluded by PLIP PG4.34: 5 residues within 4Å: Chain C: W.373, H.377, L.378, P.379, N.415 Ligand excluded by PLIP PG4.35: 5 residues within 4Å: Chain C: N.62, K.65, K.448, R.449, L.450 Ligand excluded by PLIP PG4.37: 5 residues within 4Å: Chain C: K.252, A.253, I.254, T.255, K.256 Ligand excluded by PLIP PG4.38: 2 residues within 4Å: Chain C: W.193, K.194 Ligand excluded by PLIP PG4.39: 5 residues within 4Å: Chain C: V.111, E.113, L.116, A.253, I.254 Ligand excluded by PLIP PG4.45: 7 residues within 4Å: Chain D: N.209, V.210, G.213, L.214, Q.322, H.339 Ligands: PG4.46 Ligand excluded by PLIP PG4.46: 5 residues within 4Å: Chain D: A.264, N.265, S.266, H.339 Ligands: PG4.45 Ligand excluded by PLIP PG4.47: 5 residues within 4Å: Chain D: W.373, H.377, L.378, P.379, N.415 Ligand excluded by PLIP PG4.48: 5 residues within 4Å: Chain D: N.62, K.65, K.448, R.449, L.450 Ligand excluded by PLIP PG4.50: 5 residues within 4Å: Chain D: K.252, A.253, I.254, T.255, K.256 Ligand excluded by PLIP PG4.51: 2 residues within 4Å: Chain D: W.193, K.194 Ligand excluded by PLIP PG4.52: 5 residues within 4Å: Chain D: V.111, E.113, L.116, A.253, I.254 Ligand excluded by PLIP

4 x PG6: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE(Non-covalent)

PG6.10: 10 residues within 4Å: Chain A: Y.200, M.201, K.252, K.256, K.257, P.258, D.312, W.313, P.379, I.417 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.200, A:P.258 PG6.23: 10 residues within 4Å: Chain B: Y.200, M.201, K.252, K.256, K.257, P.258, D.312, W.313, P.379, I.417 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.200, B:P.258 PG6.36: 10 residues within 4Å: Chain C: Y.200, M.201, K.252, K.256, K.257, P.258, D.312, W.313, P.379, I.417 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.200, C:P.258 PG6.49: 10 residues within 4Å: Chain D: Y.200, M.201, K.252, K.256, K.257, P.258, D.312, W.313, P.379, I.417 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.200, D:P.258

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

Related Entries With Identical Sequence