SMTL ID : 5ca3.2 (1 other biounit)

Crystal structure of the glycosynthase mutant D324N of Escherichia coli GH63 glycosidase in complex with glucose and lactose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x GLC- GAL: beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GAL.1: 12 residues within 4Å: Chain A: W.314, F.315, W.321, D.368, L.369, N.384, N.386, K.391, W.496, D.501, Y.679 Ligands: BGC.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.391, A:K.391, A:D.501, A:N.384 Water bridges: A:W.314, A:D.501, A:D.501, A:Y.679

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.431, N.433, N.435, V.437, E.439, E.549 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.431, A:V.437, A:E.439, A:E.549

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: D.538, T.540 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.538, A:T.540, H2O.14, H2O.15, H2O.17, H2O.18

1 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.4: 16 residues within 4Å: Chain A: P.308, F.315, W.321, W.323, N.324, K.391, G.499, D.501, Y.679, W.680, W.685, E.727, F.742, W.744 Ligands: GLC-GAL.1, GLC-GAL.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.323, A:N.324, A:N.324, A:G.499, A:G.499, A:E.727, A:E.727

1 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.5: 6 residues within 4Å: Chain A: T.170, D.172, K.175, Q.196, H.198, Q.241 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.172, A:K.175, A:Q.196, A:Q.241 Salt bridges: A:K.175, A:H.198

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miyazaki, T. et al., Crystal structure of the enzyme-product complex reveals sugar ring distortion during catalysis by family 63 inverting alpha-glycosidase. J.Struct.Biol. (2016)

Release Date

2016-08-10

Peptides

Glucosidase YgjK: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Glucosidase YgjK

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