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

Three-dimensional structures of two heavily N-glycosylated Aspergillus sp. Family GH3 beta-D-glucosidases

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 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.1: 12 residues within 4Å: Chain A: E.40, N.43, G.60, S.61, V.62, P.63, H.349, E.683, I.685, F.688, Y.690, W.692 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.685, A:F.688 Hydrogen bonds: A:Y.690 NAG-NAG-BMA.3: 14 residues within 4Å: Chain A: V.285, S.289, T.291, S.292, F.293, A.296, N.297, S.701, S.702, D.703, D.704, S.705, N.706 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.289, A:S.289, A:T.291, A:S.705 Water bridges: A:D.704

3 x NAG- NAG- BMA- MAN: 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(Post Translational Modification)(Non-functional Binders)

NAG-NAG-BMA-MAN.2: 13 residues within 4Å: Chain A: Y.6, S.7, P.8, V.202, D.203, D.204, I.233, N.234, E.243, T.244, V.809, S.810, Q.812 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.204 NAG-NAG-BMA-MAN.9: 13 residues within 4Å: Chain B: E.40, N.43, G.60, S.61, V.62, P.63, H.349, A.356, L.682, I.685, F.688, Y.690, W.692 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.685, B:F.688 Hydrogen bonds: B:A.356 NAG-NAG-BMA-MAN.11: 12 residues within 4Å: Chain B: V.285, S.289, T.291, S.292, F.293, N.297, S.701, S.702, D.703, D.704, S.705 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.289, B:S.289, B:S.705 Water bridges: B:T.286

2 x NAG- NAG- BMA- MAN- 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-(1-3)-[alpha-D-mannopyranose-(1-2)-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(Post Translational Modification)(Non-covalent)

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.4: 33 residues within 4Å: Chain A: Y.6, S.7, P.8, P.9, Y.11, S.195, D.196, N.235, S.236, Y.237, E.240, H.267, S.268, G.269, V.270, G.271, F.293, N.297, V.300, G.301, N.304, T.306, S.702, D.704, N.706, Y.707, G.708, W.709, K.713, Y.714, I.715, P.716 Ligands: NAG-NAG-BMA.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.706, A:G.269, A:V.270, A:D.704, A:D.704, A:D.704, A:G.708, A:W.709, A:Y.6, A:P.8, A:N.235 Water bridges: A:S.268, A:S.268 Hydrophobic interactions: A:N.297 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.12: 32 residues within 4Å: Chain B: Y.6, S.7, P.8, P.9, Y.11, S.195, D.196, N.235, S.236, E.240, H.267, S.268, G.269, V.270, G.271, F.293, N.297, V.300, G.301, N.304, T.306, S.702, D.704, N.706, Y.707, G.708, W.709, K.713, Y.714, I.715, P.716 Ligands: NAG-NAG-BMA-MAN.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.706, B:G.269, B:V.270, B:D.704, B:D.704, B:G.708, B:W.709, B:P.8, B:N.235 Water bridges: B:S.268, B:S.268 Hydrophobic interactions: B:N.297

4 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: 7 residues within 4Å: Chain A: S.411, W.412, G.421, C.422, N.424, V.496 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.14 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain A: R.684, H.686, N.694, A.700, S.701, D.703 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.684 Hydrogen bonds: A:H.686 Water bridges: A:H.686 NAG-NAG.13: 8 residues within 4Å: Chain B: S.411, W.412, G.421, C.422, N.424, V.496 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.6, NAG-NAG-BMA-MAN-MAN-MAN-MAN.14 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 6 residues within 4Å: Chain B: R.684, H.686, N.694, A.700, S.701, D.703 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.684 Hydrogen bonds: B:H.686

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

NAG-NAG-BMA-MAN-MAN-MAN.6: 14 residues within 4Å: Chain A: D.464, W.466, A.467, D.469, K.470, D.497, N.499, N.505, W.509, K.510 Chain B: W.412 Ligands: NAG-NAG.13, NAG-NAG.13, NAG-NAG-BMA-MAN-MAN-MAN-MAN.14 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.509 Hydrogen bonds: A:D.497, A:K.510, A:W.466 Water bridges: A:N.511

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.7: 17 residues within 4Å: Chain A: R.476, A.520, N.521, N.522, C.523, N.524, H.544, P.545, N.546 Chain B: T.341, D.343, Y.345, F.347, N.350, H.351, S.353, Y.357 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN-MAN-MAN.10: 13 residues within 4Å: Chain B: Y.6, S.7, P.8, V.202, D.203, D.204, I.233, N.234, E.243, T.244, V.809, S.810, Q.812 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:D.203 Hydrogen bonds: B:D.204

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: 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(Non-functional Binders)

NAG-NAG-BMA-MAN-MAN-MAN-MAN.14: 16 residues within 4Å: Chain A: W.412 Chain B: D.464, W.466, A.467, D.469, K.470, D.497, N.499, N.505, W.509, K.510 Ligands: NAG-NAG.5, NAG-NAG-BMA-MAN-MAN-MAN.6, NAG-NAG-BMA-MAN-MAN-MAN.6, NAG-NAG.13, NAG-NAG.13 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.509, B:K.510 Hydrogen bonds: B:D.497, B:K.510 Water bridges: B:N.511

1 x NAG- NAG- BMA- MAN- MAN: 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-functional Binders)

NAG-NAG-BMA-MAN-MAN.15: 13 residues within 4Å: Chain A: T.341, D.343, F.347, N.350, Y.357 Chain B: A.520, N.521, N.522, C.523, N.524, H.544, P.545, N.546 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:W.340, A:N.350, A:N.350 Water bridges: A:D.343, B:R.476

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

NAG.17: 1 residues within 4Å: Chain A: N.524 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:N.524, B:E.344 NAG.18: 2 residues within 4Å: Chain A: N.193, N.601 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.193, A:N.601 NAG.25: 2 residues within 4Å: Chain B: A.478, N.524 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.478

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.19: 5 residues within 4Å: Chain A: D.620, K.776, Y.824, S.829, R.830 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.776, A:R.830 PEG.24: 7 residues within 4Å: Chain A: W.50, D.74, R.80, W.263, D.419, S.433, Y.493 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.80, A:R.80 Water bridges: A:S.433 PEG.26: 6 residues within 4Å: Chain B: W.50, D.74, R.80, W.263, S.433, Y.493 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.74, B:R.80, B:R.80 Water bridges: B:S.433

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.21: 1 residues within 4Å: Chain A: D.543 No protein-ligand interaction detected (PLIP)

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.22: 3 residues within 4Å: Chain A: L.644, H.645, V.646 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.644, A:V.646 Salt bridges: A:H.645

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

CL.23: 2 residues within 4Å: Chain A: R.342, N.437 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain B: R.342, N.437 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Agirre, J. et al., Three-Dimensional Structures of Two Heavily N-Glycosylated Aspergillus Sp. Family Gh3 Beta-D-Glucosidases. Acta Crystallogr.,Sect.D (2016)

Release Date

2016-02-10

Peptides

BETA-GLUCOSIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

BETA-GLUCOSIDASE

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