SMTL ID : 6q6k.1

Crystal structure of recombinant human beta-glucocerebrosidase in complex with cyclophellitol activity based probe with Cy5 tag (ME569)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-dimer

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: 4 residues within 4Å: Chain A: I.5, N.19, T.21, Y.22 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: I.5, N.19, Y.22 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.22

20 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 3 residues within 4Å: Chain A: R.131, P.150, E.151 Ligand excluded by PLIP ACT.4: 2 residues within 4Å: Chain A: H.274, N.275 Ligand excluded by PLIP ACT.5: 4 residues within 4Å: Chain A: P.71, E.72, A.476, R.496 Ligand excluded by PLIP ACT.6: 3 residues within 4Å: Chain A: T.187, K.194, S.196 Ligand excluded by PLIP ACT.7: 6 residues within 4Å: Chain A: E.235, S.237, A.238, D.283, Q.284 Ligands: ACT.33 Ligand excluded by PLIP ACT.8: 4 residues within 4Å: Chain A: K.321, G.325, Y.373, H.374 Ligand excluded by PLIP ACT.9: 2 residues within 4Å: Chain A: Q.207, R.211 Ligand excluded by PLIP ACT.10: 2 residues within 4Å: Chain A: S.45, R.47 Ligand excluded by PLIP ACT.11: 3 residues within 4Å: Chain A: A.438, N.442, L.444 Ligand excluded by PLIP ACT.29: 1 residues within 4Å: Chain A: S.8 Ligand excluded by PLIP ACT.30: 5 residues within 4Å: Chain A: F.75, Q.76, H.328, H.374 Ligands: ACT.32 Ligand excluded by PLIP ACT.31: 5 residues within 4Å: Chain A: D.24, S.25, F.26, R.48, Y.418 Ligand excluded by PLIP ACT.32: 4 residues within 4Å: Chain A: F.75, H.328, H.374 Ligands: ACT.30 Ligand excluded by PLIP ACT.33: 1 residues within 4Å: Ligands: ACT.7 Ligand excluded by PLIP ACT.34: 2 residues within 4Å: Chain B: E.254, R.257 Ligand excluded by PLIP ACT.35: 3 residues within 4Å: Chain B: T.187, K.198, G.199 Ligand excluded by PLIP ACT.36: 2 residues within 4Å: Chain B: H.290, K.293 Ligand excluded by PLIP ACT.37: 1 residues within 4Å: Chain B: Q.207 Ligand excluded by PLIP ACT.38: 2 residues within 4Å: Chain B: H.274, N.275 Ligand excluded by PLIP ACT.52: 1 residues within 4Å: Ligands: NAG.39 Ligand excluded by PLIP

27 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 Ligand excluded by PLIP SO4.13: 2 residues within 4Å: Chain A: R.44, S.45 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain A: K.79, W.228, R.277, H.306 Ligand excluded by PLIP SO4.15: 1 residues within 4Å: Chain A: K.473 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain A: Y.11, W.348, E.349, Q.350, R.353 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain A: E.254, R.257 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain A: R.44, S.465, Y.487 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain A: H.290, K.293 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain A: E.111, R.170, P.428 Ligand excluded by PLIP SO4.21: 2 residues within 4Å: Chain A: S.464, S.465 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain A: Q.226, T.272, H.273, V.276 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain A: R.277, V.305, H.306 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain A: F.331, P.332, N.333, T.334 Ligand excluded by PLIP SO4.25: 7 residues within 4Å: Chain A: D.453, G.454, S.455, W.494, H.495, R.496, Q.497 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain A: T.187, K.198, G.199 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain A: R.285, P.319, A.320, T.369 Ligand excluded by PLIP SO4.40: 6 residues within 4Å: Chain B: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP SO4.41: 2 residues within 4Å: Chain B: R.44, S.45 Ligand excluded by PLIP SO4.42: 4 residues within 4Å: Chain B: G.193, K.194, S.242, G.243 Ligand excluded by PLIP SO4.43: 4 residues within 4Å: Chain B: K.79, W.228, R.277, H.306 Ligand excluded by PLIP SO4.44: 3 residues within 4Å: Chain B: R.44, S.465, Y.487 Ligand excluded by PLIP SO4.45: 3 residues within 4Å: Chain B: I.158, P.159, H.162 Ligand excluded by PLIP SO4.46: 2 residues within 4Å: Chain B: K.321, R.329 Ligand excluded by PLIP SO4.47: 3 residues within 4Å: Chain B: R.277, V.305, H.306 Ligand excluded by PLIP SO4.48: 5 residues within 4Å: Chain B: Q.226, T.272, H.273, N.275, V.276 Ligand excluded by PLIP SO4.49: 1 residues within 4Å: Chain B: R.262 Ligand excluded by PLIP SO4.50: 2 residues within 4Å: Chain B: S.45, R.47 Ligand excluded by PLIP

2 x HKW: 6-[3,3-dimethyl-2-[(1~{E},3~{E},5~{E})-5-(1,3,3-trimethylindol-2-ylidene)penta-1,3-dienyl]indol-1-ium-1-yl]-~{N}-[[1-[[(1~{S},2~{R},3~{R},4~{S},6~{S})-2,3,4,6-tetrakis(oxidanyl)cyclohexyl]methyl]-1,2,3-triazol-4-yl]methyl]hexanamide(Covalent)

HKW.28: 25 residues within 4Å: Chain A: D.127, F.128, W.179, N.234, E.235, L.241, S.242, G.243, Y.244, P.245, F.246, Y.313, E.340, W.381, F.397, V.398 Chain B: L.314, D.315, L.317, E.349, D.358, M.361, Q.362, H.365, R.463 15 PLIP interactions: 5 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:D.358, B:M.361, B:Q.362, B:H.365, B:R.463, A:L.241, A:Y.244, A:P.245, A:E.340 Hydrogen bonds: A:D.127, A:W.179, A:N.234, A:E.235, A:E.235 Water bridges: A:E.235 HKW.51: 11 residues within 4Å: Chain B: D.127, F.128, W.179, N.234, E.235, F.246, Y.313, E.340, C.342, W.381, N.396 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:E.340 Hydrogen bonds: B:D.127, B:W.179, B:N.234, B:E.235, B:E.235, B:N.396 Water bridges: B:E.235

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

NAG.39: 3 residues within 4Å: Chain B: H.145, N.146 Ligands: ACT.52 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.146 Water bridges: B:T.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Artola, M. et al., Functionalized Cyclophellitols Are Selective Glucocerebrosidase Inhibitors and Induce a Bona Fide Neuropathic Gaucher Model in Zebrafish. J.Am.Chem.Soc. (2019)

Release Date

2019-03-27

Peptides

Glucosylceramidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glucosylceramidase

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