SMTL ID : 4iif.1

Crystal structure of beta-glucosidase 1 from Aspergillus aculeatus in complex with castanospermine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

2 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(Non-functional Binders)

NAG-NAG-BMA-MAN.1: 12 residues within 4Å: Chain A: D.38, E.39, N.42, G.59, P.62, Y.348, P.355, T.682, I.684, F.687, Y.689, W.691 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.348, A:I.684, A:F.687 Hydrogen bonds: A:Y.348 Water bridges: A:Y.348, A:Y.348 NAG-NAG-BMA-MAN.9: 14 residues within 4Å: Chain B: F.5, S.6, P.7, V.201, D.202, D.203, I.232, N.233, Y.242, T.243, V.808, A.809, Q.811 Ligands: MRD.26 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:D.202 Hydrogen bonds: B:D.203, B:Y.242, B:Y.242, B:Q.811 Water bridges: B:K.204

3 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(Post Translational Modification)(Non-covalent)

NAG-NAG-BMA.2: 12 residues within 4Å: Chain A: F.5, S.6, P.7, V.201, D.202, D.203, I.232, N.233, Y.242, T.243, V.808, A.809 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.202 Hydrogen bonds: A:D.203, A:Y.242, A:Q.811 Water bridges: A:D.202 NAG-NAG-BMA.5: 7 residues within 4Å: Chain A: E.404, Y.411, C.421, N.423, D.496, K.509 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.496 NAG-NAG-BMA.12: 9 residues within 4Å: Chain B: E.404, Y.411, C.421, N.423, D.496, K.509 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.6, NAG-NAG-BMA-MAN-MAN-MAN-MAN.6, NAG-NAG-BMA-MAN-MAN-MAN-MAN.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.496, B:D.496, B:D.496

2 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: 12 residues within 4Å: Chain A: I.284, T.290, S.291, F.292, T.295, N.296, S.700, S.701, G.702, D.703, P.704 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.284 NAG-NAG.10: 11 residues within 4Å: Chain B: I.284, T.290, S.291, F.292, N.296, S.700, S.701, G.702, D.703, P.704 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.11 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.4: 29 residues within 4Å: Chain A: S.6, P.7, P.8, S.194, D.195, S.235, Q.239, H.266, S.267, G.268, V.269, G.270, F.292, N.296, I.299, A.300, N.303, T.305, S.701, D.703, Y.705, Y.706, G.707, V.708, D.709, T.710, H.713, P.715 Ligands: NAG-NAG.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:N.296 Hydrogen bonds: A:G.268, A:V.269, A:D.703, A:G.707, A:T.710 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.11: 32 residues within 4Å: Chain B: F.5, S.6, P.7, P.8, Y.10, S.194, D.195, N.234, S.235, Q.239, H.266, S.267, G.268, V.269, G.270, F.292, N.296, I.299, A.300, N.303, T.305, S.701, D.703, Y.705, Y.706, G.707, V.708, D.709, T.710, H.713, P.715 Ligands: NAG-NAG.10 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:N.296 Hydrogen bonds: B:G.268, B:V.269, B:D.703, B:G.707, B:V.708, B:V.708 Water bridges: B:D.703

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-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.6: 12 residues within 4Å: Chain A: D.463, W.465, A.466, Q.469, D.496, N.498, N.504, W.508, K.509 Chain B: Y.411 Ligands: NAG-NAG-BMA.5, NAG-NAG-BMA.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.508 Hydrogen bonds: A:D.496, A:K.509 NAG-NAG-BMA-MAN-MAN-MAN-MAN.13: 11 residues within 4Å: Chain A: Y.411 Chain B: D.463, W.465, A.466, Q.469, D.496, N.498, N.504, W.508, K.509 Ligands: NAG-NAG-BMA.12 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:D.496, B:W.508 Hydrogen bonds: B:D.496, B:K.509 Water bridges: B:N.510

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

NAG-NAG-BMA-MAN-MAN-MAN.7: 12 residues within 4Å: Chain A: A.519, N.520, N.521, C.522, N.523, H.543, N.545 Chain B: T.340, D.342, F.349, Q.352, Y.356 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN-MAN-MAN-MAN.8: 15 residues within 4Å: Chain B: D.38, E.39, N.42, G.59, G.60, P.62, Y.348, P.355, G.680, L.681, T.682, I.684, F.687, Y.689, W.691 6 PLIP interactions: 6 interactions with chain B Water bridges: B:E.357, B:Y.348, B:Y.348 Hydrophobic interactions: B:Y.348, B:I.684, B:F.687 Hydrogen bonds: B:Y.348

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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(Post Translational Modification)

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.14: 14 residues within 4Å: Chain A: T.340, D.342, Y.344, F.346, F.349, Q.352, Y.356 Chain B: A.519, N.520, N.521, C.522, N.523, H.543, N.545 No protein-ligand interaction detected (PLIP)

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

NAG.15: 2 residues within 4Å: Chain A: N.192, N.600 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.192 NAG.16: 6 residues within 4Å: Chain A: R.683, N.693, A.699, S.700, S.701, G.702 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.683, A:N.693 NAG.21: 2 residues within 4Å: Chain B: N.192, N.600 No protein-ligand interaction detected (PLIP) NAG.22: 2 residues within 4Å: Chain B: N.639, S.641 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.641 NAG.23: 5 residues within 4Å: Chain B: R.683, N.693, A.699, S.700, G.702 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.683, B:N.693

4 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.17: 7 residues within 4Å: Chain A: G.394, E.396, R.397, H.454, K.455, G.456 Chain B: N.364 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.397 Hydrogen bonds: A:R.397, A:H.454 Water bridges: B:N.364 MRD.24: 7 residues within 4Å: Chain B: W.49, R.79, F.286, S.432, E.490, Y.492 Ligands: CTS.27 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.49, B:F.286, B:Y.492 Hydrogen bonds: B:R.79, B:R.79 MRD.25: 6 residues within 4Å: Chain B: D.80, S.338, W.339, T.340, R.341, E.436 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:D.80, B:E.436 Hydrogen bonds: B:R.341, B:R.341 Water bridges: B:E.436 MRD.26: 6 residues within 4Å: Chain B: N.200, V.201, D.202, F.607, S.608 Ligands: NAG-NAG-BMA-MAN.9 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:D.202

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.18: 6 residues within 4Å: Chain A: D.80, S.338, W.339, T.340, R.341, E.436 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.80, A:E.436 Hydrogen bonds: A:S.338, A:R.341, A:R.341 MPD.19: 5 residues within 4Å: Chain A: W.49, R.79, F.286, Y.492 Ligands: CTS.20 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.49, A:F.286, A:Y.492, A:Y.492 Hydrogen bonds: A:R.79, A:R.79

2 x CTS: CASTANOSPERMINE(Non-covalent)

CTS.20: 14 residues within 4Å: Chain A: D.73, R.79, L.122, R.137, K.170, H.171, R.181, M.226, Y.229, D.261, W.262, S.432, E.490 Ligands: MPD.19 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.262 Hydrogen bonds: A:D.73, A:R.79, A:R.137, A:R.137, A:K.170, A:K.170, A:H.171, A:R.181, A:S.432, A:E.490 Salt bridges: A:D.73, A:D.261, A:E.490 CTS.27: 15 residues within 4Å: Chain B: V.55, D.73, R.79, L.122, R.137, K.170, H.171, R.181, M.226, Y.229, D.261, W.262, S.432, E.490 Ligands: MRD.24 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:V.55, B:W.262 Hydrogen bonds: B:D.73, B:R.79, B:R.137, B:R.137, B:K.170, B:H.171, B:R.181, B:S.432, B:E.490 Water bridges: B:K.170 Salt bridges: B:D.73, B:D.261, B:E.490

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suzuki, K. et al., Crystal structures of glycoside hydrolase family 3 beta-glucosidase 1 from Aspergillus aculeatus. Biochem.J. (2013)

Release Date

2013-04-10

Peptides

Beta-glucosidase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-glucosidase 1

Related Entries With Identical Sequence