SMTL ID : 6t13.2 (1 other biounit)

CRYSTAL STRUCTURE OF GLUCOCEREBROSIDASE IN COMPLEX WITH A PYRROLOPYRAZINE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: I.44, N.58, T.60 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.58, A:N.58 NAG.13: 3 residues within 4Å: Chain B: I.44, N.58, Y.61 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.58

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: P.68, T.69, Y.79, E.150, K.464, F.465, L.532 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.69, A:Y.79, A:K.464, A:K.464, A:K.464 Water bridges: A:R.209

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

SO4.3: 6 residues within 4Å: Chain A: Y.50, S.51, R.392, S.395, W.396, D.397 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.51, A:S.51, A:S.51, A:W.396, A:D.397 Water bridges: A:R.392, A:R.392, A:R.392, A:S.395, A:D.397, A:D.397, A:R.398 Salt bridges: A:R.392 SO4.4: 4 residues within 4Å: Chain A: K.118, W.267, R.316, H.345 6 PLIP interactions: 6 interactions with chain A Water bridges: A:K.118, A:K.118, A:E.468 Salt bridges: A:K.118, A:R.316, A:H.345 SO4.5: 3 residues within 4Å: Chain A: R.83, S.84, Y.526 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.83, A:S.84 Salt bridges: A:R.83 SO4.6: 2 residues within 4Å: Chain A: H.329, K.332 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.329, A:K.332 SO4.15: 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: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.51, B:S.51, B:W.396, B:D.397, A:S.281 Water bridges: B:R.392, A:G.282 Salt bridges: B:R.392 SO4.16: 4 residues within 4Å: Chain B: K.118, W.267, R.316, H.345 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:K.118, B:R.316, B:H.345

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

TRS.7: 10 residues within 4Å: Chain A: D.166, F.167, W.218, E.274, F.285, Y.352, E.379, W.420, N.435 Ligands: M7H.14 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.218, A:E.274, A:W.420, A:N.435 Water bridges: A:N.273, A:E.274, A:S.384

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

EDO.8: 9 residues within 4Å: Chain A: C.62, D.63, S.64, L.142, K.145, S.146, E.151, G.152, K.452 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.142, A:E.151, A:K.452 Water bridges: A:S.64 EDO.9: 6 residues within 4Å: Chain A: F.48, L.393, P.426, D.444, K.447, Y.451 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.451, A:Y.451 EDO.10: 5 residues within 4Å: Chain A: D.63, S.64, F.65, R.87, Y.457 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.63, A:R.87, A:K.452 Water bridges: A:C.43 EDO.11: 5 residues within 4Å: Chain A: G.304, L.307, A.308, H.313, Y.343 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.307, A:Y.343 EDO.12: 3 residues within 4Å: Chain A: I.197, P.198, H.201 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.193, A:H.262, A:H.262

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

M7H.14: 13 residues within 4Å: Chain A: P.284, F.285, Q.323, Y.352, L.353, S.384, V.433, N.435 Chain B: D.354, S.384, W.387, E.388 Ligands: TRS.7 12 PLIP interactions: 7 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:W.387 Hydrogen bonds: A:Q.323, A:S.384 Water bridges: A:S.276, A:N.435, B:E.388 pi-Stacking: B:W.387

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

CL.17: 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
B

B
C

Glucosylceramidase

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