SMTL ID : 5ifp.1

STRUCTURE OF BETA-GALACTOSIDASE FROM ASPERGILLUS NIGER

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

monomer

Ligands

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.1: 21 residues within 4Å: Chain A: F.312, A.313, E.317, D.363, T.369, S.371, N.373, T.375, F.909, N.911, S.915, T.943, S.944, E.978, S.980, T.982, T.983 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.2, GOL.18 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.943, A:E.317, A:S.944 Water bridges: A:T.943, A:R.376, A:T.943 Hydrophobic interactions: A:F.312 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.2: 16 residues within 4Å: Chain A: E.317, N.320, N.321, E.322, R.325, T.375, E.377, S.380, N.568, Y.571, N.572, Y.603, N.622, T.983 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.377, A:N.321, A:E.322, A:R.325, A:R.325, A:E.377 Water bridges: A:N.320, A:E.322, A:T.375, A:E.377, A:S.380, A:N.572 Hydrophobic interactions: A:Y.571

1 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, R.731, N.760, K.789, T.790, Y.791, V.792 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.789, A:K.789

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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

NAG-NAG-BMA-MAN-MAN-MAN.4: 18 residues within 4Å: Chain A: W.307, G.308, G.309, Y.771, A.772, N.914, T.917, P.918, Y.935, I.936, S.937, N.938, I.939, G.940, P.941, Q.942, T.943 Ligands: GOL.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.308

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

NAG.5: 5 residues within 4Å: Chain A: N.156, T.703, K.704, N.705, T.706 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.706 Water bridges: A:N.156 NAG.6: 2 residues within 4Å: Chain A: T.283, N.402 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.402 Water bridges: A:N.402 NAG.7: 4 residues within 4Å: Chain A: S.423, N.478, S.480, G.481 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.478, A:G.481 Water bridges: A:S.480 NAG.8: 3 residues within 4Å: Chain A: N.522, V.523, Q.537 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.522, A:Q.537 NAG.9: 1 residues within 4Å: Chain A: N.739 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.739, A:N.739 NAG.10: 4 residues within 4Å: Chain A: D.746, N.773, D.775, N.777 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.775, A:N.777 Water bridges: A:D.746, A:D.775, A:N.777, A:N.821

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.11: 2 residues within 4Å: Chain A: R.827, P.828 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.827 SO4.12: 2 residues within 4Å: Chain A: Y.109, H.176 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Y.109, A:D.112, A:D.112 Salt bridges: A:H.176

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.13: 4 residues within 4Å: Chain A: R.862, Q.863, A.1006, Y.1007 Ligand excluded by PLIP

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.14: 8 residues within 4Å: Chain A: N.140, E.142, E.200, A.237, Y.260, F.264, W.806 Ligands: GOL.15 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.140, A:E.142, A:E.200, A:W.806 Water bridges: A:N.140, A:E.142, A:E.142, A:Y.260, A:E.804 Salt bridges: A:E.200

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 11 residues within 4Å: Chain A: Y.96, I.139, N.140, A.141, E.142, N.199, E.200, N.235, E.298, Y.342 Ligands: BTB.14 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.96, A:N.140, A:A.141, A:E.142, A:N.199, A:E.200, A:N.235, A:D.258, A:Y.342 Water bridges: A:E.142, A:E.200 GOL.16: 1 residues within 4Å: Chain A: K.183 No protein-ligand interaction detected (PLIP) GOL.17: 4 residues within 4Å: Chain A: K.183, Y.184, N.188, G.189 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.188 GOL.18: 8 residues within 4Å: Chain A: G.311, F.312, A.313, P.941, Q.942, T.943, S.944 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:A.313, A:P.941, A:T.943, A:S.944, A:S.944 Water bridges: A:F.312, A:F.312, A:A.314, A:T.943 GOL.19: 5 residues within 4Å: Chain A: N.357, S.751, Y.771, A.772 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.771 Water bridges: A:S.774

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rico-Diaz, A. et al., Structural features of Aspergillus niger beta-galactosidase define its activity against glycoside linkages. FEBS J. (2017)

Release Date

2017-04-19

Peptides

beta-galactosidase A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

beta-galactosidase A