SMTL ID : 5juv.1

STRUCTURE OF E298Q-BETA-GALACTOSIDASE FROM ASPERGILLUS NIGER IN COMPLEX WITH 6-b-Galactopyranosyl galactose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

monomer

Ligands

1 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: 18 residues within 4Å: Chain A: A.313, E.317, D.363, T.369, S.371, N.373, 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-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.943 Hydrogen bonds: A:E.317, A:S.944

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-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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-MAN-MAN.2: 17 residues within 4Å: Chain A: E.317, N.320, N.321, E.322, R.325, T.375, E.377, S.380, T.550, 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 4 PLIP interactions: 4 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: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: 16 residues within 4Å: Chain A: W.307, G.308, G.309, Y.771, A.772, N.914, T.917, 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 GAL- GAL: beta-D-galactopyranose-(1-6)-beta-D-galactopyranose(Non-covalent)

GAL-GAL.4: 17 residues within 4Å: Chain A: Y.96, I.139, N.140, A.141, E.142, N.199, E.200, A.237, D.258, S.259, Y.260, F.264, Q.298, Y.304, Y.342, Y.364 Ligands: 1PE.11 8 PLIP interactions: 8 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:Q.298, A:Y.364

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

NAG.5: 2 residues within 4Å: Chain A: N.156, T.706 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.706 NAG.6: 4 residues within 4Å: Chain A: S.423, N.478, S.480, G.481 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.478 NAG.7: 2 residues within 4Å: Chain A: N.739, E.740 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.739 NAG.8: 6 residues within 4Å: Chain A: S.688, R.731, N.760, T.790, Y.791, V.792 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.791 Hydrogen bonds: A:Y.690, A:R.731, A:T.790 NAG.9: 4 residues within 4Å: Chain A: D.746, N.773, D.775, N.777 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.775, A:N.777

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

CL.10: 4 residues within 4Å: Chain A: R.862, Q.863, A.1006, Y.1007 Ligand excluded by PLIP

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.11: 7 residues within 4Å: Chain A: N.140, E.142, Y.355, E.804, W.806 Ligands: GAL-GAL.4, GAL-GAL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.140, A:Y.355, A:Y.355

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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