SMTL ID : 8zrz.1

The 1.26 angstrom resolution structure of Bacillus cereus beta-amylase in complex with maltose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.26 Å

Oligo State

monomer

Ligands

3 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose

GLC-GLC.1: 15 residues within 4Å: Chain A: W.221, T.223, L.225, A.230, I.231, L.232, P.233, P.234, S.235, Q.239, F.240, G.244, Y.249 Ligands: GLC-GLC.4, GLC-GLC.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.232, A:S.235 Water bridges: A:S.235, A:S.235, A:S.235, A:D.236 GLC-GLC.2: 4 residues within 4Å: Chain A: W.449, K.482, W.495, Q.499 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.499, A:Q.499 GLC-GLC.4: 6 residues within 4Å: Chain A: S.235, D.236, Q.239 Ligands: GLC-GLC.1, GLC-GLC.1, GOL.15 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.235, A:S.235, A:Q.239

1 x BGC- GLC: alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose

BGC-GLC.3: 3 residues within 4Å: Chain A: N.33, W.37, Q.40 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.40, A:Q.40, A:Q.40, A:N.33, A:N.33 Water bridges: A:N.33, A:N.33, A:D.34, A:D.34, A:D.34, A:N.405, A:N.405

1 x GLC- GLC- GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose

GLC-GLC-GLC-GLC.5: 26 residues within 4Å: Chain A: M.16, L.19, D.49, W.51, I.85, H.89, N.94, V.95, D.97, A.170, E.172, R.174, Y.178, Y.186, K.287, A.289, G.290, H.292, W.293, T.330, C.331, E.367, A.369, L.370, L.396, R.397 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:H.89, A:D.97, A:R.397, A:R.397 Water bridges: A:A.17, A:A.17, A:D.49, A:D.49, A:Q.90, A:G.92, A:D.97

1 x CA: CALCIUM ION

CA.6: 5 residues within 4Å: Chain A: E.56, D.60, Q.61, E.141, E.144 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.56, A:D.60, A:E.141, A:E.144, H2O.2

1 x SO4: SULFATE ION

SO4.7: 1 residues within 4Å: Chain A: R.468 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.468, A:R.468, A:R.468, A:R.468 Salt bridges: A:R.468

8 x GOL: GLYCEROL

GOL.8: 2 residues within 4Å: Chain A: D.60, Q.61 No protein-ligand interaction detected (PLIP) GOL.9: 2 residues within 4Å: Chain A: K.219, G.222 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.219 GOL.10: 4 residues within 4Å: Chain A: D.277, Q.281, V.282, P.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.277 Water bridges: A:H.273, A:D.277 GOL.11: 4 residues within 4Å: Chain A: T.431, Y.460, N.465, W.467 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.465 Water bridges: A:V.429, A:T.431, A:N.465, A:N.465 GOL.12: 2 residues within 4Å: Chain A: Y.195, K.200 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.200 Water bridges: A:K.119, A:E.197 GOL.13: 4 residues within 4Å: Chain A: Y.313, S.314, N.352, L.356 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.352 Water bridges: A:Y.313, A:S.314, A:S.314 GOL.14: 5 residues within 4Å: Chain A: S.188, Q.294, N.297, P.341, Y.343 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.188, A:Q.294, A:Q.294, A:N.297 Water bridges: A:R.189 GOL.15: 4 residues within 4Å: Chain A: G.222, T.223, K.224 Ligands: GLC-GLC.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.224 Water bridges: A:G.222

1 x BGC: beta-D-glucopyranose

BGC.16: 5 residues within 4Å: Chain A: S.501, W.502, S.511, H.512, T.513 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.511, A:T.513, A:T.513, A:T.513 Water bridges: A:W.502 Salt bridges: A:H.512

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hirata, A. et al., Structural insight into sugar-binding modes of microbial ss-amylase. Biochem.Biophys.Res.Commun. (2024)

Release Date

2024-09-25

Peptides

Beta-amylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-amylase

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