SMTL ID : 4iug.1

Crystal structure of beta-galactosidase from Aspergillus oryzae in complex with galactose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-BMA-MAN-MAN.1: 18 residues within 4Å: Chain A: E.313, D.363, T.369, E.370, T.371, N.373, T.375, R.376, P.907, Y.909, N.911, S.942, S.974, E.976, T.980, T.981 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.2, CD.19 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.911, A:T.941, A:E.313, A:E.313, A:R.376, A:S.942

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-BMA-MAN-MAN-MAN-MAN.2: 16 residues within 4Å: Chain A: Y.316, A.317, N.320, H.321, E.322, R.325, T.375, E.377, S.380, R.567, N.568, Y.571, Y.603, N.622, T.981 Ligands: NAG-NAG-BMA-MAN-MAN.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.377, A:E.377, A:E.322, A:R.325, A:R.325, A:R.567, A:E.377 Hydrophobic interactions: A:Y.571 Water bridges: A:T.375, A:E.377, A:S.380

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 8 residues within 4Å: Chain A: S.688, Y.690, N.760, E.786, K.789, N.790, Y.791, V.792 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.790 NAG-NAG.4: 5 residues within 4Å: Chain A: R.746, A.773, D.775, N.777 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.746, A:R.746

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.5: 21 residues within 4Å: Chain A: D.265, A.267, P.306, G.308, G.309, P.310, A.770, D.771, Y.772, N.914, T.916, F.933, T.934, G.935, N.936, V.937, G.938, P.939, Q.940, T.941 Ligands: NAG-NAG.4 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.771, A:G.308, A:D.771

1 x BMA- BMA- NAG- BMA- NAG- M6D- NAG- BMA- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-6-O-phosphono-beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose(Non-covalent)

BMA-BMA-NAG-BMA-NAG-M6D-NAG-BMA-NAG.6: 18 residues within 4Å: Chain A: L.79, R.110, E.112, G.113, A.116, P.119, D.122, E.126, T.583, H.609, T.618, K.848, V.849, E.994 Ligands: CD.7, CD.8, CD.34, CD.35 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.618, A:D.122

29 x CD: CADMIUM ION(Non-covalent)(Non-functional Binders)

CD.7: 4 residues within 4Å: Chain A: E.126 Ligands: BMA-BMA-NAG-BMA-NAG-M6D-NAG-BMA-NAG.6, BMA-BMA-NAG-BMA-NAG-M6D-NAG-BMA-NAG.6, CD.34 Ligand excluded by PLIP CD.8: 2 residues within 4Å: Chain A: E.112 Ligands: BMA-BMA-NAG-BMA-NAG-M6D-NAG-BMA-NAG.6 Ligand excluded by PLIP CD.9: 3 residues within 4Å: Chain A: M.774, D.803, N.815 Ligand excluded by PLIP CD.10: 2 residues within 4Å: Chain A: E.460, V.534 Ligand excluded by PLIP CD.11: 3 residues within 4Å: Chain A: E.460, H.512, D.547 Ligand excluded by PLIP CD.12: 1 residues within 4Å: Chain A: D.40 Ligand excluded by PLIP CD.13: 1 residues within 4Å: Chain A: D.122 Ligand excluded by PLIP CD.14: 4 residues within 4Å: Chain A: N.140, E.142, E.804 Ligands: GAL.36 Ligand excluded by PLIP CD.15: 2 residues within 4Å: Chain A: T.158, D.163 Ligand excluded by PLIP CD.16: 1 residues within 4Å: Chain A: D.214 Ligand excluded by PLIP CD.17: 1 residues within 4Å: Chain A: T.249 Ligand excluded by PLIP CD.18: 1 residues within 4Å: Chain A: D.227 Ligand excluded by PLIP CD.19: 2 residues within 4Å: Chain A: E.313 Ligands: NAG-NAG-BMA-MAN-MAN.1 Ligand excluded by PLIP CD.20: 2 residues within 4Å: Chain A: E.322, Q.438 Ligand excluded by PLIP CD.21: 1 residues within 4Å: Chain A: D.410 Ligand excluded by PLIP CD.22: 2 residues within 4Å: Chain A: D.410, K.446 Ligand excluded by PLIP CD.23: 1 residues within 4Å: Chain A: D.413 Ligand excluded by PLIP CD.24: 1 residues within 4Å: Chain A: D.530 Ligand excluded by PLIP CD.25: 1 residues within 4Å: Chain A: D.614 Ligand excluded by PLIP CD.26: 1 residues within 4Å: Chain A: E.644 Ligand excluded by PLIP CD.27: 1 residues within 4Å: Chain A: D.676 Ligand excluded by PLIP CD.28: 1 residues within 4Å: Chain A: D.699 Ligand excluded by PLIP CD.29: 1 residues within 4Å: Chain A: D.711 Ligand excluded by PLIP CD.30: 2 residues within 4Å: Chain A: H.707, N.815 Ligand excluded by PLIP CD.31: 2 residues within 4Å: Chain A: H.355, G.357 Ligand excluded by PLIP CD.32: 2 residues within 4Å: Chain A: D.828, S.830 Ligand excluded by PLIP CD.33: 2 residues within 4Å: Chain A: K.105, D.844 Ligand excluded by PLIP CD.34: 3 residues within 4Å: Ligands: BMA-BMA-NAG-BMA-NAG-M6D-NAG-BMA-NAG.6, BMA-BMA-NAG-BMA-NAG-M6D-NAG-BMA-NAG.6, CD.7 Ligand excluded by PLIP CD.35: 3 residues within 4Å: Chain A: E.991 Ligands: BMA-BMA-NAG-BMA-NAG-M6D-NAG-BMA-NAG.6, BMA-BMA-NAG-BMA-NAG-M6D-NAG-BMA-NAG.6 Ligand excluded by PLIP

1 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.36: 16 residues within 4Å: Chain A: Y.96, I.139, N.140, A.141, E.142, N.199, E.200, N.235, D.258, Y.260, E.298, F.304, Y.342, Y.362, Y.364 Ligands: CD.14 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.96, A:N.140, A:A.141, A:N.199, A:E.200, A:N.235, A:D.258, A:D.258, A:Y.260

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.37: 4 residues within 4Å: Chain A: D.279, N.280, N.402, L.403 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.279, A:L.403

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maksimainen, M.M. et al., The crystal structure of acidic beta-galactosidase from Aspergillus oryzae. Int.J.Biol.Macromol. (2013)

Release Date

2013-07-31

Peptides

Beta-galactosidase A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-galactosidase A