SMTL ID : 7cwi.1

Crystal structure of beta-galactosidase II from Bacillus circulans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: R.142, H.336, N.403, E.404, N.467, E.489, W.550, E.558 Ligands: GOL.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.142, A:R.142, A:N.403, A:E.404, A:N.467, A:E.558 Water bridges: A:H.302, A:Y.555, A:E.558 GOL.2: 5 residues within 4Å: Chain A: H.459, H.480, P.481, N.482, W.483 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.459, A:H.480, A:N.482, A:W.483 GOL.3: 4 residues within 4Å: Chain A: K.191, K.384, D.388, I.427 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.191, A:K.191, A:D.388, A:D.388 Water bridges: A:K.384 GOL.4: 6 residues within 4Å: Chain A: Y.91, F.108, S.140, C.361, D.370, Y.371 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.91, A:Y.371 Water bridges: A:D.360, A:D.360, A:D.360 GOL.5: 6 residues within 4Å: Chain A: E.404, D.438, R.441, Y.468, W.527 Ligands: GOL.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.404, A:R.441, A:R.441 Water bridges: A:W.527 GOL.6: 3 residues within 4Å: Chain A: R.377, W.378, H.381 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.381 GOL.7: 3 residues within 4Å: Chain A: K.191, T.231, H.233 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.191, A:T.231, A:H.233

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 6 residues within 4Å: Chain A: D.540, L.541, K.542, H.543, S.644, W.645 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.542, A:H.543, A:S.644 Salt bridges: A:H.543 SO4.9: 3 residues within 4Å: Chain A: K.594, K.595, E.596 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.595, A:E.596 Salt bridges: A:K.594 SO4.10: 4 residues within 4Å: Chain A: F.6, D.8, N.9, K.70 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.5, A:K.70, A:T.73 Salt bridges: A:K.70 SO4.11: 4 residues within 4Å: Chain A: E.380, R.422, W.423, E.426 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.423 Salt bridges: A:R.422 SO4.12: 1 residues within 4Å: Chain A: R.21 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.133 Salt bridges: A:R.21, A:K.133 SO4.13: 3 residues within 4Å: Chain A: K.25, P.26, S.27 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.27, A:S.27 Salt bridges: A:K.25

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.14: 5 residues within 4Å: Chain A: F.274, G.275, N.392, E.393, P.394 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Choi, J.Y. et al., High Galacto-Oligosaccharide Production and a Structural Model for Transgalactosylation of beta-Galactosidase II from Bacillus circulans . J.Agric.Food Chem. (2020)

Release Date

2020-12-09

Peptides

beta-galactosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

beta-galactosidase

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