SMTL ID : 4xpr.1

Crystal structure of the mutant D365A of Pedobacter saltans GH31 alpha-galactosidase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 9 residues within 4Å: Chain A: Y.101, V.110, H.111, F.451, G.534, M.535, L.537, E.567, I.568 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.568, A:I.568 Water bridges: A:M.535 EDO.2: 8 residues within 4Å: Chain A: Y.516, S.519, A.520, R.523, G.575, D.576, D.577, F.663 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.516, A:S.519, A:D.576, A:D.576, A:D.577, A:D.577 EDO.3: 6 residues within 4Å: Chain A: H.123, Y.371, Y.374, R.419, D.435 Ligands: EDO.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.370, A:R.419, A:R.419 EDO.4: 3 residues within 4Å: Chain A: F.602, R.654, Y.656 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.654 EDO.5: 7 residues within 4Å: Chain A: E.267, W.306, K.364, Y.433, D.435, N.485, W.487 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.267, A:K.364, A:D.435, A:N.485 Water bridges: A:Y.433, A:D.435 EDO.6: 5 residues within 4Å: Chain A: H.123, Y.371, D.435, Y.436 Ligands: EDO.3 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.371, A:Y.371 EDO.7: 9 residues within 4Å: Chain B: Y.101, V.110, H.111, F.451, G.534, M.535, L.537, E.567, I.568 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.568, B:I.568 Water bridges: B:M.535 EDO.8: 8 residues within 4Å: Chain B: Y.516, S.519, A.520, R.523, G.575, D.576, D.577, F.663 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.516, B:S.519, B:D.576, B:D.577 EDO.9: 6 residues within 4Å: Chain B: H.123, Y.371, Y.374, R.419, D.435 Ligands: EDO.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.370, B:R.419, B:R.419, B:D.435 EDO.10: 3 residues within 4Å: Chain B: F.602, R.654, Y.656 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.654, B:Y.656 EDO.11: 7 residues within 4Å: Chain B: E.267, W.306, K.364, Y.433, D.435, N.485, W.487 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.267, B:K.364, B:D.435, B:N.485 EDO.12: 5 residues within 4Å: Chain B: H.123, Y.371, D.435, Y.436 Ligands: EDO.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.371

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miyazaki, T. et al., Structural and biochemical characterization of novel bacterial alpha-galactosidases belonging to glycoside hydrolase family 31. Biochem.J. (2015)

Release Date

2015-05-20

Peptides

Alpha-glucosidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Alpha-glucosidase

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