SMTL ID : 6t13.1 (1 other biounit)

CRYSTAL STRUCTURE OF GLUCOCEREBROSIDASE IN COMPLEX WITH A PYRROLOPYRAZINE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

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.44, N.58, T.60, Y.61 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.61

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

SO4.2: 7 residues within 4Å: Chain A: Y.50, S.51, R.392, S.395, W.396, D.397 Ligands: EDO.9 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.51, A:S.51, A:S.395, A:W.396, A:D.397 Water bridges: A:R.392, A:R.392, A:R.392 Salt bridges: A:R.392 SO4.3: 4 residues within 4Å: Chain A: K.118, W.267, R.316, H.345 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.267 Water bridges: A:R.316 Salt bridges: A:K.118, A:R.316, A:H.345 SO4.4: 2 residues within 4Å: Chain A: R.83, S.84 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.84, A:S.84 Salt bridges: A:R.83 SO4.5: 3 residues within 4Å: Chain A: H.329, K.332 Chain B: P.358 5 PLIP interactions: 5 interactions with chain A Water bridges: A:H.329, A:H.329, A:H.329 Salt bridges: A:H.329, A:K.332 SO4.12: 7 residues within 4Å: Chain A: S.281 Chain B: Y.50, S.51, R.392, S.395, W.396, D.397 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.51, B:S.51, B:S.51, B:W.396, B:D.397, A:S.281 Water bridges: B:R.392 Salt bridges: B:R.392 SO4.13: 4 residues within 4Å: Chain B: K.118, W.267, R.316, H.345 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:W.267 Water bridges: B:K.118, B:R.316, B:R.316, B:R.316 Salt bridges: B:K.118, B:R.316, B:H.345 SO4.14: 3 residues within 4Å: Chain A: G.232, G.282 Chain B: R.392 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:N.231, A:K.233, A:G.282, B:R.392 Salt bridges: B:R.392 SO4.15: 2 residues within 4Å: Chain B: H.329, K.332 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.332 Salt bridges: B:H.329, B:K.332

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.6: 10 residues within 4Å: Chain A: D.166, F.167, W.218, E.274, Y.283, F.285, E.379, W.420, N.435 Ligands: M7H.11 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:W.218, A:E.274, A:W.420, A:N.435 Water bridges: A:N.273, A:Y.283, A:Y.283, A:S.384

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

EDO.7: 5 residues within 4Å: Chain A: A.97, K.512, D.513, P.514, G.517 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.513 Water bridges: A:N.98 EDO.8: 5 residues within 4Å: Chain A: D.63, S.64, F.65, R.87, Y.457 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.63 Water bridges: A:C.43, A:D.63, A:R.87, A:K.452 EDO.9: 7 residues within 4Å: Chain A: R.392, S.395, D.397, R.398, Q.401 Chain B: S.281 Ligands: SO4.2 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.398, A:R.398, A:Q.401, B:S.281 Water bridges: A:E.388, B:S.281 EDO.17: 6 residues within 4Å: Chain B: P.42, C.43, G.85, R.86, R.87, E.89 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.43, B:R.87

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

NAG.10: 4 residues within 4Å: Chain B: I.44, N.58, T.60, Y.61 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.58, B:T.60

1 x M7H: 1-[4-[2-(4-methoxyphenyl)-5-methyl-pyrrolo[2,3-b]pyrazin-6-yl]piperidin-1-yl]ethanone(Non-covalent)

M7H.11: 15 residues within 4Å: Chain A: P.284, F.285, Q.323, Y.352, L.353, S.384, V.433, R.434, N.435 Chain B: D.354, F.355, S.384, W.387, E.388 Ligands: TRS.6 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:P.284, A:F.285, A:N.435, B:W.387, B:W.387, B:E.388 Hydrogen bonds: A:S.384 Water bridges: A:Q.323, A:N.435, B:E.388 pi-Stacking: B:W.387

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.16: 5 residues within 4Å: Chain B: Q.323, R.324, H.350, W.351, Y.352 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Benz, J. et al., Novel beta-Glucocerebrosidase Activators That Bind to a New Pocket at a Dimer Interface and Induce Dimerization. Angew.Chem.Int.Ed.Engl. (2021)

Release Date

2020-12-23

Peptides

Glucosylceramidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Glucosylceramidase

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