SMTL ID : 5i3d.1

Sulfolobus solfataricus beta-glycosidase - E387Y mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

homo-tetramer

Ligands

15 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 6 residues within 4Å: Chain A: W.151, E.206, Y.322, W.361, Y.387 Ligands: ACT.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.322, A:W.361 Water bridges: A:Y.387 ACT.2: 5 residues within 4Å: Chain A: F.359, W.361, E.432, W.433 Ligands: ACT.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.434 ACT.3: 8 residues within 4Å: Chain A: W.84, F.88, L.92, L.118, W.156, E.182, R.185, F.186 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.88, A:L.118, A:F.186 Hydrogen bonds: A:W.84, A:E.182, A:F.186 Salt bridges: A:R.185 ACT.4: 4 residues within 4Å: Chain A: E.279, E.282, W.287, K.374 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.374 Water bridges: A:E.279, A:K.374 Salt bridges: A:K.374 ACT.5: 4 residues within 4Å: Chain B: E.464, N.468 Chain C: R.463 Ligands: ACT.6 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Salt bridges: C:R.463 Hydrogen bonds: B:N.468 ACT.6: 7 residues within 4Å: Chain B: E.464, E.474 Chain C: K.72, W.455, L.460, R.463 Ligands: ACT.5 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.455, C:L.460 Water bridges: C:R.463, C:R.463, B:E.464 Salt bridges: C:K.72, C:R.463 ACT.7: 5 residues within 4Å: Chain B: E.206, Y.322, W.361, Y.387 Ligands: ACT.8 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.322, B:W.361 Hydrogen bonds: B:Y.387 Water bridges: B:N.320, B:N.320, B:Y.387 ACT.8: 5 residues within 4Å: Chain B: F.359, W.361, E.432, W.433 Ligands: ACT.7 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.434 ACT.9: 8 residues within 4Å: Chain B: W.84, F.88, L.92, L.118, W.156, E.182, R.185, F.186 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.88, B:L.118, B:F.186 Hydrogen bonds: B:W.84, B:E.182, B:F.186 Salt bridges: B:R.185 ACT.11: 5 residues within 4Å: Chain C: E.206, Y.322, W.361, Y.387 Ligands: ACT.12 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.322, C:W.361 ACT.12: 5 residues within 4Å: Chain C: F.222, F.359, E.432, W.433 Ligands: ACT.11 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.222 Hydrogen bonds: C:E.432 Water bridges: C:E.432, C:A.434 ACT.13: 8 residues within 4Å: Chain C: W.84, F.88, L.92, L.118, W.156, E.182, R.185, F.186 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.88, C:L.118, C:F.186 Hydrogen bonds: C:F.186 Salt bridges: C:R.185 ACT.14: 6 residues within 4Å: Chain D: W.151, E.206, Y.322, W.361, Y.387 Ligands: ACT.15 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Y.322, D:W.361 Water bridges: D:Y.322 ACT.15: 4 residues within 4Å: Chain D: F.359, E.432, W.433 Ligands: ACT.14 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.432 Water bridges: D:E.432, D:A.434 ACT.16: 8 residues within 4Å: Chain D: W.84, F.88, L.92, L.118, W.156, E.182, R.185, F.186 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.88, D:L.118, D:F.186 Hydrogen bonds: D:F.186 Salt bridges: D:R.185

1 x PE8: 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL(Non-covalent)

PE8.10: 6 residues within 4Å: Chain C: E.112, N.113, K.116, D.119, E.120, W.192 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.112, C:K.116 Water bridges: C:R.117, C:R.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iglesias-Fernandez, J. et al., A front-face 'SNi synthase' engineered from a retaining 'double-SN2' hydrolase. Nat. Chem. Biol. (2017)

Release Date

2017-02-01

Peptides

Beta-galactosidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
A

D
C

Beta-galactosidase