SMTL ID : 5fji.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 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(Post Translational Modification)

NAG-NAG-BMA-MAN-MAN-MAN-MAN.1: 14 residues within 4Å: Chain A: E.39, N.42, G.59, S.60, P.62, E.348, H.349, G.355, A.356, T.358, I.687, F.690, Y.692, W.694 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.687, A:F.690 Hydrogen bonds: A:Y.692 NAG-NAG-BMA-MAN-MAN-MAN-MAN.8: 14 residues within 4Å: Chain B: E.39, N.42, G.59, S.60, P.62, E.348, H.349, G.355, A.356, T.358, I.687, F.690, Y.692, W.694 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.687, B:F.690 Hydrogen bonds: B:Y.692

2 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(Non-functional Binders)

NAG-NAG-BMA-MAN-MAN-MAN.2: 16 residues within 4Å: Chain A: F.5, S.6, P.7, V.202, D.203, D.204, I.233, N.234, Q.243, T.244, K.247, K.731, V.811, E.812, A.813, Q.814 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.204, A:K.247 Water bridges: A:D.203, A:K.247, A:K.247 NAG-NAG-BMA-MAN-MAN-MAN.9: 16 residues within 4Å: Chain B: F.5, S.6, P.7, V.202, D.203, D.204, I.233, N.234, Q.243, T.244, K.247, K.731, V.811, E.812, A.813, Q.814 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.204, B:K.247 Water bridges: B:K.205, B:K.247, B:K.247

4 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(Non-functional Binders)

NAG-NAG-BMA.3: 13 residues within 4Å: Chain A: L.291, S.292, F.293, N.297, S.703, S.704, D.705, D.706, P.707 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.4, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.4, NAG.16, EDO.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.705 NAG-NAG-BMA.7: 7 residues within 4Å: Chain A: V.520, S.521, H.522, C.523, N.524, N.544, N.546 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 14 residues within 4Å: Chain B: I.285, L.291, S.292, F.293, N.297, S.703, S.704, D.705, D.706, P.707 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.11, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.11, NAG.41, EDO.46 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.705 NAG-NAG-BMA.14: 7 residues within 4Å: Chain B: V.520, S.521, H.522, C.523, N.524, N.544, N.546 No protein-ligand interaction detected (PLIP)

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(Non-functional Binders)

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.4: 33 residues within 4Å: Chain A: S.6, P.7, P.8, Y.10, E.196, N.235, S.236, Y.237, Q.240, H.267, S.268, G.269, V.270, G.271, F.293, N.297, V.300, S.301, N.304, T.306, S.704, D.706, N.708, Y.709, G.710, W.711, E.715, Y.716, I.717, P.718 Ligands: NAG-NAG-BMA.3, NAG-NAG-BMA.3, IMD.36 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.708, A:P.7, A:N.235, A:G.269, A:V.270, A:D.706, A:G.710, A:W.711 Water bridges: A:S.268, A:N.708 Hydrophobic interactions: A:N.297 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.11: 34 residues within 4Å: Chain B: F.5, S.6, P.7, P.8, Y.10, E.196, N.235, S.236, Y.237, Q.240, H.267, S.268, G.269, V.270, G.271, F.293, N.297, V.300, S.301, N.304, T.306, S.704, D.706, N.708, Y.709, G.710, W.711, E.715, Y.716, I.717, P.718 Ligands: NAG-NAG-BMA.10, NAG-NAG-BMA.10, EDO.42 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.708, B:P.7, B:N.235, B:G.269, B:V.270, B:D.706, B:G.710, B:W.711 Hydrophobic interactions: B:N.297 Water bridges: B:N.708

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.5: 7 residues within 4Å: Chain A: P.411, W.412, C.422, N.424 Chain B: D.464 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.6, EDO.39 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.497

2 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(Post Translational Modification)(Non-functional Binders)

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.6: 16 residues within 4Å: Chain A: G.466, A.467, S.469, Q.470, D.497, N.499, K.504, N.505, T.507, W.509, K.510, N.511 Chain B: W.412 Ligands: NAG-NAG-BMA-MAN.5, NAG-NAG-BMA-MAN.5, NAG-NAG-BMA-MAN-MAN.12 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:D.497 Hydrogen bonds: A:D.497, A:K.510 Water bridges: A:D.497, A:N.511, A:N.511 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.13: 15 residues within 4Å: Chain A: W.412 Chain B: G.466, A.467, S.469, Q.470, D.497, N.499, K.504, N.505, T.507, W.509, K.510, N.511 Ligands: NAG-NAG-BMA-MAN-MAN.12, NAG-NAG-BMA-MAN-MAN.12 8 PLIP interactions: 8 interactions with chain B Water bridges: B:N.511, B:N.511, B:G.512, B:E.513 Hydrophobic interactions: B:D.497, B:W.509 Hydrogen bonds: B:D.497, B:K.510, B:N.511

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

NAG-NAG-BMA-MAN-MAN.12: 10 residues within 4Å: Chain A: D.464 Chain B: P.411, W.412, C.417, G.421, C.422, N.424 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.6, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.13, EDO.64 No protein-ligand interaction detected (PLIP)

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

NAG.15: 1 residues within 4Å: Chain A: N.524 No protein-ligand interaction detected (PLIP) NAG.16: 6 residues within 4Å: Chain A: R.686, N.696, D.702, S.703, D.705 Ligands: NAG-NAG-BMA.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.705 Hydrogen bonds: A:R.686, A:N.696 NAG.40: 1 residues within 4Å: Chain B: N.524 No protein-ligand interaction detected (PLIP) NAG.41: 6 residues within 4Å: Chain B: R.686, N.696, D.702, S.703, D.705 Ligands: NAG-NAG-BMA.10 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.705 Hydrogen bonds: B:R.686, B:N.696

39 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.17: 2 residues within 4Å: Chain A: Q.477 Chain B: N.415 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: E.451, N.455, Y.569 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: Q.446, R.450 Chain B: Q.446, R.450 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: R.375, Y.440, E.559, N.562 Chain B: I.453 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain A: F.81, S.339, W.340, T.341, R.342, N.437 Ligands: EDO.26 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain A: S.33, Q.34, M.35, T.36, G.670, E.671 Ligand excluded by PLIP EDO.23: 9 residues within 4Å: Chain A: G.290, G.295, T.296, Y.680, R.686, F.690, I.691, Y.692 Ligands: NAG-NAG-BMA.3 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain A: L.64, G.65, I.66, Y.323, Y.324, D.329 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain A: W.49, R.80, S.433, F.493 Ligands: EDO.34 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain A: E.50, F.81, S.339, W.340 Ligands: EDO.21 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain A: D.16, K.250, A.251, G.254, T.663 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain A: Y.636, T.637, G.757, N.758, V.759 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain A: R.27, Y.324, G.327, D.329, R.330 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain A: K.108, D.163 Ligands: EDO.33 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain A: R.645, Q.647, R.748, V.749, S.750 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain A: G.395, K.396, E.397, N.455, G.456, G.457 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain A: Q.162, D.163, V.326, L.331 Ligands: EDO.30 Ligand excluded by PLIP EDO.34: 8 residues within 4Å: Chain A: D.74, L.123, K.171, M.227, D.262, W.263, S.433 Ligands: EDO.25 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain A: Q.183, Y.230, W.263, S.264, F.287 Ligand excluded by PLIP EDO.39: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN.5 Ligand excluded by PLIP EDO.42: 6 residues within 4Å: Chain B: S.264, H.266, H.267, I.285, F.293 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.11 Ligand excluded by PLIP EDO.43: 2 residues within 4Å: Chain A: N.415 Chain B: Q.477 Ligand excluded by PLIP EDO.44: 6 residues within 4Å: Chain B: I.31, G.65, Y.323, Y.324, D.329 Ligands: EDO.58 Ligand excluded by PLIP EDO.45: 5 residues within 4Å: Chain B: K.100, V.152, R.782, K.783, F.784 Ligand excluded by PLIP EDO.46: 8 residues within 4Å: Chain B: G.290, G.295, T.296, Y.680, F.690, I.691, Y.692 Ligands: NAG-NAG-BMA.10 Ligand excluded by PLIP EDO.47: 5 residues within 4Å: Chain A: I.453 Chain B: R.375, Y.440, E.559, N.562 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain B: W.49, R.80, S.433, F.493 Ligands: EDO.49 Ligand excluded by PLIP EDO.49: 8 residues within 4Å: Chain B: D.74, L.123, K.171, M.227, D.262, W.263, S.433 Ligands: EDO.48 Ligand excluded by PLIP EDO.50: 4 residues within 4Å: Chain B: K.250, A.251, G.254, T.663 Ligand excluded by PLIP EDO.51: 3 residues within 4Å: Chain B: Y.104, K.108, D.163 Ligand excluded by PLIP EDO.52: 6 residues within 4Å: Chain B: S.33, Q.34, M.35, T.36, G.670, E.671 Ligand excluded by PLIP EDO.53: 3 residues within 4Å: Chain B: T.819, K.820, Y.821 Ligand excluded by PLIP EDO.54: 4 residues within 4Å: Chain B: R.645, Q.647, R.748, S.750 Ligand excluded by PLIP EDO.55: 5 residues within 4Å: Chain B: D.99, T.101, L.102, E.376, R.786 Ligand excluded by PLIP EDO.56: 2 residues within 4Å: Chain B: Y.762, F.788 Ligand excluded by PLIP EDO.57: 4 residues within 4Å: Chain B: R.53, P.335, K.359, D.362 Ligand excluded by PLIP EDO.58: 4 residues within 4Å: Chain B: R.27, E.30, Y.324 Ligands: EDO.44 Ligand excluded by PLIP EDO.59: 4 residues within 4Å: Chain B: T.394, E.451, N.455, Y.569 Ligand excluded by PLIP EDO.64: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN.12 Ligand excluded by PLIP

7 x IMD: IMIDAZOLE(Non-covalent)

IMD.36: 3 residues within 4Å: Chain A: W.711, E.715 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.4 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:W.711 IMD.37: 4 residues within 4Å: Chain A: N.365, Q.367, R.368 Chain B: G.456 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.365, A:R.368 IMD.38: 5 residues within 4Å: Chain A: N.304, G.305, T.306, D.713, R.722 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.304, A:T.306 IMD.60: 5 residues within 4Å: Chain B: N.201, D.203, D.607, F.608, N.609 3 PLIP interactions: 3 interactions with chain B Water bridges: B:V.202, B:V.202, B:D.203 IMD.61: 4 residues within 4Å: Chain A: G.456 Chain B: N.365, Q.367, R.368 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.365, B:R.368 IMD.62: 7 residues within 4Å: Chain B: G.395, K.396, E.397, V.398, N.455, G.456, G.457 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.455 IMD.63: 3 residues within 4Å: Chain B: Q.162, D.163, K.325 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.162, B:K.325

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