SMTL ID : 6lge.1

Bombyx mori GH13 sucrose hydrolase complexed with acarbose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x BGC- GLC- AC1: 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose

BGC-GLC-AC1.1: 20 residues within 4Å: Chain A: D.94, Y.97, H.137, Q.183, F.184, F.203, Q.207, R.237, D.239, A.240, Y.243, E.314, Y.316, I.344, T.345, H.380, D.381, N.382, R.447, R.451 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.94, A:H.137, A:Q.207, A:R.237, A:R.237, A:Y.243, A:E.314, A:E.314, A:R.447, A:R.447, A:R.451, A:N.382, A:D.381, A:N.382 Water bridges: A:D.94, A:E.314, A:E.314, A:Y.316, A:Q.183, A:Y.243 BGC-GLC-AC1.2: 20 residues within 4Å: Chain B: D.94, Y.97, H.137, Q.183, F.184, F.203, Q.207, R.237, D.239, A.240, Y.243, E.314, Y.316, I.344, T.345, H.380, D.381, N.382, R.447, R.451 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.94, B:D.94, B:H.137, B:Q.207, B:R.237, B:R.237, B:D.239, B:Y.243, B:Y.243, B:E.314, B:R.447, B:R.447, B:R.451, B:N.382, B:Y.243, B:D.381, B:N.382 Water bridges: B:D.94, B:E.314, B:Y.316, B:D.381, B:D.381, B:Q.183, B:Y.243

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

MG.3: 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.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain A: H.556 No protein-ligand interaction detected (PLIP) MG.7: 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.14

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 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.1, H2O.5 CA.8: 5 residues within 4Å: Chain B: N.136, D.209, Y.243, L.244, E.246 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.209, B:Y.243, B:L.244, B:E.246, H2O.15

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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