SMTL ID : 5ihr.1

STRUCTURE OF E298Q-BETA-GALACTOSIDASE FROM ASPERGILLUS NIGER IN COMPLEX WITH ALLOLACTOSE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 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: 22 residues within 4Å: Chain A: F.312, A.313, E.317, D.363, T.369, S.371, N.373, T.375, R.376, 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, DMS.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.943, A:E.317, A:R.376, A:S.944 Water bridges: 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.377, A:N.321, A:R.325, A:R.325, A:E.377 Hydrophobic interactions: A:Y.571 Water bridges: A:T.375, A:E.377, A:S.380

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.3: 17 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.308

1 x GLC- GAL: beta-D-galactopyranose-(1-6)-alpha-D-glucopyranose(Non-covalent)

GLC-GAL.4: 15 residues within 4Å: Chain A: Y.96, I.139, N.140, A.141, E.142, N.199, E.200, A.237, Y.260, Q.298, Y.304, Y.342, Y.362, Y.364, W.806 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.96, A:Y.96, A:N.140, A:A.141, A:N.199, A:E.200, A:Q.298 Water bridges: A:E.142

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

NAG.5: 4 residues within 4Å: Chain A: N.156, T.703, N.705, T.706 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.706 NAG.6: 3 residues within 4Å: Chain A: S.423, N.478, G.481 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.478, A:G.481 NAG.7: 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.8: 1 residues within 4Å: Chain A: N.739 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.739 NAG.9: 7 residues within 4Å: Chain A: S.688, Y.690, R.731, N.760, T.790, Y.791, V.792 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.791 Hydrogen bonds: A:Y.690, A:R.731, A:N.760, A:T.790 NAG.10: 5 residues within 4Å: Chain A: D.746, N.773, D.775, N.777, N.821 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.775, A:N.777 Water bridges: A:N.777

1 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

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

CL.12: 3 residues within 4Å: Chain A: R.862, Q.863, Y.1007 Ligand excluded by PLIP

9 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.13: 5 residues within 4Å: Chain A: N.572, A.601, T.624, T.625, S.626 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.626 DMS.14: 6 residues within 4Å: Chain A: N.914, S.915, T.943 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.1 No protein-ligand interaction detected (PLIP) DMS.15: 7 residues within 4Å: Chain A: A.744, I.745, D.746, N.777, N.821, F.822, L.823 No protein-ligand interaction detected (PLIP) DMS.16: 3 residues within 4Å: Chain A: R.154, K.704 Ligands: DMS.20 No protein-ligand interaction detected (PLIP) DMS.17: 2 residues within 4Å: Chain A: G.452, S.453 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.453 DMS.18: 4 residues within 4Å: Chain A: K.183, Y.184, N.188, G.189 No protein-ligand interaction detected (PLIP) DMS.19: 4 residues within 4Å: Chain A: Y.679, S.878, G.883, L.884 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.679 DMS.20: 5 residues within 4Å: Chain A: P.106, W.151, R.154, V.155 Ligands: DMS.16 No protein-ligand interaction detected (PLIP) DMS.21: 1 residues within 4Å: Chain A: N.663 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.664

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

Probable beta-galactosidase A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Probable beta-galactosidase A

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