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

Structure of recombinant human beta-glucocerebrosidase in complex with azide tagged cyclophellitol epoxide inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 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: 5 residues within 4Å: Chain A: R.2, I.5, N.19, T.21, Y.22 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.22

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

NAG.2: 3 residues within 4Å: Chain A: T.138, H.145, N.146 No protein-ligand interaction detected (PLIP)

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

SO4.3: 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.356, A:W.357, A:D.358 Salt bridges: A:R.353 SO4.4: 5 residues within 4Å: Chain A: K.79, W.228, R.277, H.306 Ligands: EDO.13 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.228 Water bridges: A:K.79 Salt bridges: A:K.79, A:R.277, A:H.306 SO4.5: 2 residues within 4Å: Chain A: K.321, R.329 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.321, A:R.329 SO4.6: 3 residues within 4Å: Chain A: R.44, S.45, Y.487 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.44, A:S.45 Salt bridges: A:R.44 SO4.7: 6 residues within 4Å: Chain A: N.188, G.193, K.194, S.242, G.243, Y.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.194, A:G.243 SO4.8: 3 residues within 4Å: Chain A: R.44, S.465, Y.487 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.44 SO4.9: 1 residues within 4Å: Chain A: R.277 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.277

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

EDO.10: 8 residues within 4Å: Chain A: G.265, L.268, A.269, H.274, V.276, R.277, L.278, Y.304 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.278 EDO.11: 6 residues within 4Å: Chain A: L.94, A.95, L.96, S.97, P.98, Q.101 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.101, A:Q.101, A:Q.101 EDO.12: 7 residues within 4Å: Chain A: L.67, L.436, A.438, N.442, L.444, D.445, A.446 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.442, A:N.442 Water bridges: A:N.442 EDO.13: 6 residues within 4Å: Chain A: K.77, V.78, K.79, E.429, G.430 Ligands: SO4.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.429 Water bridges: A:K.77 EDO.14: 3 residues within 4Å: Chain A: E.111, R.170, P.428 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.170, A:R.170 EDO.15: 3 residues within 4Å: Chain A: K.198, G.199, Y.205 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.199 EDO.16: 8 residues within 4Å: Chain A: E.235, S.237, A.238, L.241, Y.244, D.283, Q.284, Y.313 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.237 EDO.17: 1 residues within 4Å: Chain A: R.329 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.329, A:R.329

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.18: 7 residues within 4Å: Chain A: P.3, C.4, P.6, G.46, R.47, R.48, E.50 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.4, A:G.46, A:R.48 Water bridges: A:R.47 GOL.19: 13 residues within 4Å: Chain A: A.1, R.2, P.3, C.4, D.24, S.25, F.26, R.48, M.49, E.50, K.413, F.417, Y.418 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:C.4, A:D.24, A:R.48, A:R.48 Water bridges: A:D.24, A:L.51, A:K.413

1 x PN8: (1~{S},2~{R},3~{R},4~{S},5~{S})-4-[[($l^{5}-azanylidyne-$l^{5}-azanyl)amino]methyl]cyclohexane-1,2,3,5-tetrol(Covalent)

PN8.20: 15 residues within 4Å: Chain A: C.126, D.127, F.128, W.179, N.234, E.235, F.246, H.311, Y.313, E.340, C.342, W.381, N.392, N.396, V.398 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.340 Hydrogen bonds: A:D.127, A:W.179, A:N.234, A:E.235, A:W.381, A:N.396, A:N.396

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rowland, R.J. et al., Design, Synthesis and Structural Analysis of Glucocerebrosidase Imaging Agents. Chemistry (2021)

Release Date

2021-05-12

Peptides

Glucosylceramidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Glucosylceramidase

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