SMTL ID : 6lgi.1

Bombyx mori GH13 sucrose hydrolase mutant E322Q covalent intermediate complexed with fructose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

5 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.2 MG.3: 1 residues within 4Å: Ligands: FRU.5 No protein-ligand interaction detected (PLIP) MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 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.20 MG.11: 1 residues within 4Å: Ligands: FRU.13 No protein-ligand interaction detected (PLIP)

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.2, H2O.5 CA.10: 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.19, H2O.25

2 x BGC: beta-D-glucopyranose(Post Translational Modification)

BGC.4: 14 residues within 4Å: Chain A: D.94, Y.97, H.137, F.184, F.203, Q.207, R.237, D.239, Q.314, H.380, D.381, R.447, R.451 Ligands: FRU.5 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.94, A:D.94, A:H.137, A:Q.207, A:R.237, A:R.237, A:H.380, A:H.380, A:R.447, A:R.447, A:R.451 BGC.12: 14 residues within 4Å: Chain B: D.94, Y.97, H.137, F.184, F.203, Q.207, R.237, D.239, Q.314, H.380, D.381, R.447, R.451 Ligands: FRU.13 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.94, B:H.137, B:Q.207, B:R.237, B:R.237, B:H.380, B:H.380, B:R.447, B:R.447, B:R.451

2 x FRU: beta-D-fructofuranose(Non-covalent)

FRU.5: 9 residues within 4Å: Chain A: F.203, A.240, Q.314, Y.316, D.381, E.432, R.447 Ligands: MG.3, BGC.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.314, A:Q.314, A:Y.316, A:Y.316, A:E.432, A:R.447 Water bridges: A:Y.243, A:D.381, A:D.381, A:R.436 FRU.13: 10 residues within 4Å: Chain B: F.203, D.239, A.240, Q.314, Y.316, D.381, E.432, R.447 Ligands: MG.11, BGC.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.314, B:Q.314, B:Y.316, B:E.432

2 x BDF: beta-D-fructopyranose(Non-covalent)

BDF.6: 8 residues within 4Å: Chain A: F.212, R.213, K.218, I.245, E.285, D.288, V.289, E.292 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.218 BDF.14: 8 residues within 4Å: Chain B: F.212, R.213, K.218, I.245, E.285, D.288, V.289, E.292 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.218 Water bridges: B:R.213, B:R.213

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

ACT.7: 7 residues within 4Å: Chain A: W.83, R.237, Q.314, F.339, F.341, V.376, N.379 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.83, A:F.339, A:F.341, A:V.376 Hydrogen bonds: A:N.379 Water bridges: A:Q.314, A:Q.314 Salt bridges: A:R.237 ACT.15: 6 residues within 4Å: Chain B: W.83, R.237, Q.314, F.339, F.341, N.379 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.83, B:F.339, B:F.341 Hydrogen bonds: B:N.379 Water bridges: B:Q.314, B:Q.314 Salt bridges: B:R.237

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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