SMTL ID : 5nbs.1 (1 other biounit)

Structural studies of a Glycoside Hydrolase Family 3 beta-glucosidase from the Model Fungus Neurospora crassa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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.1: 16 residues within 4Å: Chain A: E.54, N.57, G.74, A.75, I.76, P.77, H.364, D.370, Y.371, Q.372, F.698, P.699, V.701, F.704, Y.706, Y.708 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.701, A:F.704

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.2: 14 residues within 4Å: Chain A: Y.19, S.20, E.21, I.216, D.217, D.218, A.247, N.248, K.257, R.745, T.827, V.828, K.829, Q.830 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.218, A:K.257, A:K.257, A:T.827 Water bridges: A:K.219, A:N.261, A:Q.830 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.4: 28 residues within 4Å: Chain A: Y.19, S.20, E.21, P.22, Y.24, E.210, S.250, Q.254, H.281, S.282, G.283, V.284, A.285, Y.307, N.311, A.315, N.318, T.320, S.718, D.720, Q.722, Y.723, G.724, Q.725, F.730, L.731, P.732 Ligands: NAG-NAG-BMA-MAN.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.282, A:Q.722, A:Q.722, A:Q.725, A:G.283, A:V.284, A:D.720, A:G.724, A:Q.725 Water bridges: A:Q.722, A:S.282, A:A.285, A:Q.722, A:Q.725 Hydrophobic interactions: A:N.311

1 x NAG- NAG- BMA- MAN: 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.3: 13 residues within 4Å: Chain A: T.299, R.305, S.306, Y.307, T.310, N.311, S.717, S.718, G.719, D.720, A.721 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.4, NAG.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.721

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.5: 3 residues within 4Å: Chain A: N.538, N.539 Ligands: NAG-NAG-BMA.7 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN.6: 13 residues within 4Å: Chain A: R.477, H.479, A.480, P.481, T.482, E.483, D.511, N.513, N.519, T.521, W.523, N.524, E.525 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:D.511, A:W.523 Hydrogen bonds: A:D.511, A:D.511, A:N.524 Water bridges: A:E.525

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.7: 8 residues within 4Å: Chain A: S.534, S.535, W.536, C.537, N.538, N.558, N.560 Ligands: NAG-NAG.5 No protein-ligand interaction detected (PLIP)

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

NAG.8: 2 residues within 4Å: Chain A: N.207, N.615 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.207 Water bridges: A:N.207, A:N.207 NAG.9: 1 residues within 4Å: Chain A: N.637 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.848 NAG.10: 4 residues within 4Å: Chain A: L.425, C.435, N.436, N.437 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.436 Hydrogen bonds: A:N.436 NAG.11: 8 residues within 4Å: Chain A: N.478, H.479, P.481, E.525, A.528, L.529, N.532, W.536 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.528 Hydrogen bonds: A:H.479, A:N.532 NAG.12: 5 residues within 4Å: Chain A: R.305, Y.700, N.710, S.717 Ligands: NAG-NAG-BMA-MAN.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.305, A:R.305, A:R.305, A:N.710

Links

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Citation

Karkehabadi, S. et al., Structural studies of a glycoside hydrolase family 3 beta-glucosidase from the model fungus Neurospora crassa. Acta Crystallogr F Struct Biol Commun (2018)

Release Date

2018-03-21

Peptides

Beta-glucosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-glucosidase

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