SMTL ID : 6lga.1

Bombyx mori GH13 sucrose hydrolase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 5 residues within 4Å: Chain A: D.55, D.57, D.59, I.61, D.63 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.55, A:D.57, A:D.59, A:I.61, A:D.63, H2O.1 MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.8: 5 residues within 4Å: Chain B: D.55, D.57, D.59, I.61, D.63 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.55, B:D.57, B:D.59, B:I.61, B:D.63, H2O.31

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: N.136, D.209, Y.243, L.244, E.246 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.209, A:L.244, A:E.246, H2O.3, H2O.5 CA.9: 5 residues within 4Å: Chain B: N.136, D.209, Y.243, L.244, E.246 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.209, B:L.244, B:E.246, H2O.28, H2O.29

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: D.94, Y.97, V.134, H.137, F.184, Q.207, D.239, R.447 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.137, A:D.239, A:R.447, A:R.447 Water bridges: A:R.237 GOL.5: 5 residues within 4Å: Chain A: Y.316, T.345, D.381, N.382 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.382, A:N.382 GOL.6: 5 residues within 4Å: Chain A: D.381, E.432, Y.445, R.447 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.432 Water bridges: A:N.383 GOL.10: 7 residues within 4Å: Chain B: D.94, Y.97, H.380, D.381, R.447, R.451 Ligands: GOL.11 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.94, B:D.381, B:R.447, B:R.447, B:R.451 Water bridges: B:Y.97, B:Y.97, B:H.380, B:H.380 GOL.11: 9 residues within 4Å: Chain B: D.94, Y.97, V.134, H.137, F.203, Q.207, D.239, E.314 Ligands: GOL.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.137, B:Q.207, B:E.314 Water bridges: B:R.237

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 7 residues within 4Å: Chain A: G.154, Y.155, F.158, A.216, Q.219, E.220, N.223 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miyazaki, T. et al., Structure-function analysis of silkworm sucrose hydrolase uncovers the mechanism of substrate specificity in GH13 subfamily 17exo-alpha-glucosidases. J.Biol.Chem. (2020)

Release Date

2020-05-20

Peptides

Sucrose hydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Sucrose hydrolase

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