SMTL ID : 8p3e.1

Crystal structure of glucocerebrosidase in complex with allosteric activator

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

2 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: 5 residues within 4Å: Chain B: R.2, I.5, N.19, T.21, Y.22 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.22 NAG-NAG.5: 5 residues within 4Å: Chain D: R.2, I.5, N.19, T.21, Y.22 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.22

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

NAG.2: 5 residues within 4Å: Chain A: I.5, N.19, T.21, Y.22 Ligands: NAG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.19, A:T.21 NAG.3: 3 residues within 4Å: Chain A: R.2, Y.22 Ligands: NAG.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.22 NAG.6: 5 residues within 4Å: Chain C: I.5, N.19, T.21, Y.22 Ligands: NAG.7 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.19, C:T.21 NAG.7: 3 residues within 4Å: Chain C: R.2, Y.22 Ligands: NAG.6 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.22

2 x WSI: 2-[[3-[(4-chlorophenyl)carbamoyl]phenyl]sulfonylamino]benzoic acid(Non-covalent)

WSI.4: 10 residues within 4Å: Chain B: Q.73, F.75, R.433, G.435, L.436, V.437, A.438, N.442, L.444, A.446 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.75, B:V.437, B:A.438 Hydrogen bonds: B:L.436, B:A.438 Water bridges: B:L.436 Salt bridges: B:R.433 Halogen bonds: B:L.444 WSI.8: 10 residues within 4Å: Chain D: Q.73, F.75, R.433, G.435, L.436, V.437, A.438, N.442, L.444, A.446 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.75, D:V.437, D:A.438 Hydrogen bonds: D:L.436, D:A.438 Water bridges: D:L.436 Salt bridges: D:R.433 Halogen bonds: D:L.444

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schulze, M.E.D. et al., Identification of ss-Glucocerebrosidase Activators for Glucosylceramide hydrolysis. Chemmedchem (2024)

Release Date

2024-03-06

Peptides

Glucosylceramidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Glucosylceramidase

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