SMTL ID : 6moz.2 (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: 4 residues within 4Å: Chain A: I.5, N.19, T.21, Y.22 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.19, A:T.21, A:T.21

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

NA.2: 5 residues within 4Å: Chain A: Y.108, Y.116, D.380, L.383, P.401 Ligand excluded by PLIP NA.3: 7 residues within 4Å: Chain A: C.4, I.5, C.16, V.17, C.18, Y.22, D.24 Ligand excluded by PLIP NA.4: 6 residues within 4Å: Chain A: R.353, S.356, R.359, D.399, Q.414, M.416 Ligand excluded by PLIP NA.5: 5 residues within 4Å: Chain A: F.37, P.55, Q.57, F.479, E.481 Ligand excluded by PLIP NA.6: 4 residues within 4Å: Chain A: T.36, M.53, G.54, P.55 Ligand excluded by PLIP NA.7: 5 residues within 4Å: Chain A: N.234, E.235, Y.244, F.246 Ligands: GOL.19 Ligand excluded by PLIP NA.8: 6 residues within 4Å: Chain A: P.32, A.33, L.34, T.36, W.494, H.495 Ligand excluded by PLIP NA.9: 3 residues within 4Å: Chain A: D.141, F.142, Q.143 Ligand excluded by PLIP NA.10: 3 residues within 4Å: Chain A: Q.226, T.272, H.273 Ligand excluded by PLIP NA.11: 3 residues within 4Å: Chain A: H.451, P.452, D.453 Ligand excluded by PLIP NA.12: 2 residues within 4Å: Chain A: H.290, K.293 Ligand excluded by PLIP NA.13: 5 residues within 4Å: Chain A: W.381, N.382, L.385, V.398, D.399 Ligand excluded by PLIP NA.14: 6 residues within 4Å: Chain A: K.186, N.188, N.192, G.193, G.195, C.248 Ligand excluded by PLIP NA.15: 6 residues within 4Å: Chain A: P.178, W.209, A.232, E.233, L.249, F.251 Ligand excluded by PLIP NA.16: 2 residues within 4Å: Chain A: P.253, E.254 Ligand excluded by PLIP NA.17: 3 residues within 4Å: Chain A: Y.135, N.146, S.148 Ligand excluded by PLIP NA.18: 2 residues within 4Å: Chain A: L.94, L.96 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.19: 7 residues within 4Å: Chain A: D.127, F.128, W.179, E.235, E.340, W.381 Ligands: NA.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.179, A:N.234, A:E.235, A:W.381

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

PO4.20: 6 residues within 4Å: Chain A: Y.11, S.12, R.353, S.356, W.357, D.358 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.12, A:S.12, A:S.356, A:S.356, A:W.357, A:D.358 Water bridges: A:S.356 Salt bridges: A:R.353 PO4.21: 5 residues within 4Å: Chain A: K.79, W.228, R.277, H.306, M.335 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.228, A:W.228 Water bridges: A:E.429 Salt bridges: A:K.79, A:H.306 PO4.22: 1 residues within 4Å: Chain A: K.408 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.408

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
B

Glucosylceramidase

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