SMTL ID : 6q1p.1 (2 other biounits)

Glucocerebrosidase in complex with pharmacological chaperone norIMX8

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain A: I.5, N.19, T.21, Y.22 No protein-ligand interaction detected (PLIP)

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.2: 2 residues within 4Å: Chain A: A.58, N.59 No protein-ligand interaction detected (PLIP)

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

EDO.3: 2 residues within 4Å: Chain A: H.290, K.293 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.290 EDO.4: 2 residues within 4Å: Chain A: E.254, R.257 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.257, A:R.257 EDO.5: 1 residues within 4Å: Chain A: R.277 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.277, A:R.277 EDO.6: 3 residues within 4Å: Chain A: T.187, K.198, G.199 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.198, A:K.198, A:G.199 EDO.7: 4 residues within 4Å: Chain A: R.285, P.319, A.320, T.369 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.285, A:A.320 EDO.8: 5 residues within 4Å: Chain A: D.24, S.25, F.26, R.48, Y.418 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.24 EDO.9: 3 residues within 4Å: Chain A: F.75, H.328, H.374 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.374 EDO.10: 5 residues within 4Å: Chain A: H.60, G.62, T.63, G.64, L.66 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.62 EDO.11: 2 residues within 4Å: Chain A: S.45, R.47 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.45 Water bridges: A:S.45, A:R.47

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.12: 6 residues within 4Å: Chain A: Y.11, S.12, R.353, S.356, W.357, D.358 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.12, A:S.12, A:S.12, A:W.357, A:D.358 Salt bridges: A:R.353 SO4.13: 4 residues within 4Å: Chain A: K.79, W.228, R.277, H.306 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.79 Salt bridges: A:K.79, A:R.277, A:H.306 SO4.14: 2 residues within 4Å: Chain A: R.44, S.45 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.44, A:S.45 Salt bridges: A:R.44 SO4.15: 3 residues within 4Å: Chain A: R.44, S.465, Y.487 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.487 Salt bridges: A:R.44 SO4.16: 2 residues within 4Å: Chain A: R.170, P.428 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.170 SO4.17: 2 residues within 4Å: Chain A: A.1, R.2 No protein-ligand interaction detected (PLIP)

1 x P8Y: (2S,3S,4S,5R)-2-{[(4-methylpentyl)sulfonyl]methyl}piperidine-3,4,5-triol(Non-covalent)

P8Y.18: 11 residues within 4Å: Chain A: D.127, F.128, W.179, E.235, Y.244, F.246, Q.284, Y.313, E.340, W.381, N.396 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.244, A:F.246, A:F.246 Hydrogen bonds: A:D.127, A:E.235, A:Y.313, A:N.396

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Santana, A.G. et al., Pharmacological chaperones for GCase that switch conformation with pH enhance enzyme levels in Gaucher animal models. To Be Published

Release Date

2020-08-19

Peptides

Glucosylceramidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glucosylceramidase

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