SMTL ID : 6kj0.1 (1 other biounit)

Bifunctional xylosidase/glucosidase LXYL mutant E529Q C2221

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG-MAN.1: 8 residues within 4Å: Chain A: E.77, E.78, N.81, G.95, A.96, V.97, T.98, E.104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.98 NAG-NAG-MAN.10: 8 residues within 4Å: Chain B: E.77, E.78, N.81, G.95, A.96, V.97, T.98, E.104 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: 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.2: 11 residues within 4Å: Chain A: V.240, D.241, D.242, I.271, N.272, N.279, K.281, V.772, V.773, D.774, Q.775 4 PLIP interactions: 4 interactions with chain A Water bridges: A:D.241, A:L.243 Hydrogen bonds: A:D.242, A:K.281, A:K.281 NAG-NAG-BMA-MAN-MAN-MAN-MAN.11: 11 residues within 4Å: Chain B: V.240, D.241, D.242, I.271, N.272, N.279, K.281, V.772, V.773, D.774, Q.775 4 PLIP interactions: 4 interactions with chain B Water bridges: B:D.241, B:L.243 Hydrogen bonds: B:D.242, B:K.281, B:K.281

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

NAG-NAG-BMA-MAN.3: 12 residues within 4Å: Chain A: C.444, N.448, S.449, A.450, C.451, D.452, I.453, N.455, N.457, Y.526, E.528, G.540 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.449, A:I.453 NAG-NAG-BMA-MAN.12: 12 residues within 4Å: Chain B: C.444, N.448, S.449, A.450, C.451, D.452, I.453, N.455, N.457, Y.526, E.528, G.540 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.449, B:I.453, B:E.528

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

NAG.4: 3 residues within 4Å: Chain A: E.338, N.342, T.344 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.338, A:E.338, A:N.342 NAG.5: 4 residues within 4Å: Chain A: L.325, P.382, T.383, N.385 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.325 Hydrogen bonds: A:P.382 Water bridges: A:N.385 NAG.6: 6 residues within 4Å: Chain A: V.550, T.551, S.553, S.554, N.574, N.576 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.554, A:N.574, A:N.576 Water bridges: A:Y.552 NAG.7: 1 residues within 4Å: Chain A: N.635 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.635 Water bridges: A:N.239, A:N.635 NAG.13: 3 residues within 4Å: Chain B: E.338, N.342, T.344 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.338, B:N.342 NAG.14: 4 residues within 4Å: Chain B: L.325, P.382, T.383, N.385 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.325 Hydrogen bonds: B:P.382 Water bridges: B:N.385 NAG.15: 6 residues within 4Å: Chain B: V.550, T.551, S.553, S.554, N.574, N.576 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.554, B:N.574, B:N.576 Water bridges: B:Y.552 NAG.16: 1 residues within 4Å: Chain B: N.635 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.635 Water bridges: B:N.239, B:N.635

2 x BKR: Deacetyltaxol(Non-covalent)

BKR.8: 19 residues within 4Å: Chain A: R.115, R.218, L.220, I.222, I.224, V.227, Q.229, W.301, F.324, L.325, A.327, L.328, T.383, A.447, S.449, G.465, S.466, Q.529 Ligands: XYP.9 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.220, A:I.222, A:I.222, A:I.224, A:I.224, A:V.227, A:W.301, A:F.324, A:L.325, A:A.327, A:T.383, A:A.447 Hydrogen bonds: A:R.218, A:S.466, A:S.466, A:S.466 BKR.17: 19 residues within 4Å: Chain B: R.115, R.218, L.220, I.222, I.224, V.227, Q.229, W.301, F.324, L.325, A.327, L.328, T.383, A.447, S.449, G.465, S.466, Q.529 Ligands: XYP.18 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.220, B:I.222, B:I.222, B:I.224, B:I.224, B:V.227, B:W.301, B:F.324, B:L.325, B:A.327, B:T.383, B:A.447 Hydrogen bonds: B:R.218, B:S.466, B:S.466, B:S.466 Water bridges: B:T.383

2 x XYP: beta-D-xylopyranose(Non-covalent)

XYP.9: 12 residues within 4Å: Chain A: D.109, L.158, R.174, K.207, H.208, R.218, Y.268, D.300, W.301, S.466, Q.529 Ligands: BKR.8 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.109, A:R.174, A:R.174, A:K.207, A:H.208, A:H.208, A:Y.268, A:S.466 Water bridges: A:K.207 Salt bridges: A:R.174, A:R.218 XYP.18: 12 residues within 4Å: Chain B: D.109, L.158, R.174, K.207, H.208, R.218, Y.268, D.300, W.301, S.466, Q.529 Ligands: BKR.17 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.109, B:R.174, B:R.174, B:K.207, B:H.208, B:H.208, B:S.466 Water bridges: B:K.207 Salt bridges: B:R.174, B:R.218

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, L.Y. et al., Structures of beta-glycosidase LXYL-P1-2 reveals the product binding state of GH3 family and a specific pocket for Taxol recognition. Commun Biol (2020)

Release Date

2020-02-26

Peptides

Beta-D-xylosidase/beta-D-glucosidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Beta-D-xylosidase/beta-D-glucosidase

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