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

Structure of acid-beta-glucosidase in complex with an aromatic pyrrolidine iminosugar inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.19, T.21, Y.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.19

15 x NA: SODIUM ION(Non-functional Binders)

NA.2: 5 residues within 4Å: Chain A: A.124, Y.133, Y.135, D.153, K.157 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.124, A:Y.135, A:D.153, A:K.157 NA.3: 6 residues within 4Å: Chain A: V.172, S.173, L.174, Q.226, F.227, W.228 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.172, A:L.174, A:W.228 NA.4: 5 residues within 4Å: Chain A: V.460, S.484, S.488, I.489, H.490 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.488, A:H.490 NA.5: 7 residues within 4Å: Chain A: S.8, F.9, G.10, Y.11, S.13, L.354, G.355 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.8, A:F.9, A:Y.11 NA.6: 6 residues within 4Å: Chain A: D.443, L.444, D.445, L.461, N.462, R.463 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.445, A:L.461, A:R.463, A:R.463 NA.7: 4 residues within 4Å: Chain A: L.66, T.68, V.437, S.439 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.66, A:T.68, A:T.68 NA.8: 6 residues within 4Å: Chain A: M.123, A.124, T.180, W.209, Y.212 Ligands: NA.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.123 NA.9: 7 residues within 4Å: Chain A: Q.284, R.285, H.311, W.312, Y.313, L.314, D.315 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.285, A:H.311, A:L.314, A:D.315 NA.10: 6 residues within 4Å: Chain A: C.342, W.381, N.382, L.385, V.398, D.399 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.382, A:N.382, A:N.382 NA.11: 1 residues within 4Å: Chain A: T.132 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.132, A:T.132 NA.12: 6 residues within 4Å: Chain A: T.86, D.87, P.122, C.126, F.128, S.129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.87, A:D.87 NA.13: 4 residues within 4Å: Chain A: Y.108, Y.116, D.380, L.383 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.116, A:D.380 NA.14: 3 residues within 4Å: Chain A: H.451, D.453, S.455 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.453, A:S.455 NA.15: 6 residues within 4Å: Chain A: M.123, A.124, S.125, W.179, T.180 Ligands: NA.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.125, A:W.179, A:T.180 NA.16: 3 residues within 4Å: Chain A: Y.135, N.146, S.148 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.135, A:S.148

1 x JXA: (2R,3S,4R)-2-{[4-(3,5-dichlorophenyl)-1H-1,2,3-triazol-1-yl]methyl}pyrrolidine-3,4-diol(Non-covalent)

JXA.17: 15 residues within 4Å: Chain A: D.127, F.128, W.179, N.234, E.235, Y.244, F.246, Q.284, Y.313, L.314, E.340, S.345, K.346, W.381, N.396 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.313, A:L.314 Hydrogen bonds: A:D.127, A:D.127, A:E.340, A:S.345, A:N.396 Water bridges: A:Y.244 pi-Stacking: A:Y.313

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

PO4.18: 6 residues within 4Å: Chain A: Y.11, S.12, R.353, S.356, W.357, D.358 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.12, A:S.12, A:S.12, A:W.357, A:D.358 Water bridges: A:S.356 Salt bridges: A:R.353 PO4.19: 5 residues within 4Å: Chain A: V.214, D.218, S.271, T.272, H.273 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.218, A:T.272 PO4.20: 4 residues within 4Å: Chain A: K.79, W.228, R.277, H.306 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.228, A:W.228 Salt bridges: A:K.79, A:R.277, A:H.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martinez-Bailen, M. et al., Exploring substituent diversity on pyrrolidine-aryltriazole iminosugars: Structural basis of beta-glucocerebrosidase inhibition. Bioorg.Chem. (2019)

Release Date

2019-06-19

Peptides

Glucosylceramidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glucosylceramidase

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