SMTL ID : 6yv3.2 (1 other biounit)

Structure of recombinant human beta-glucocerebrosidase in complex with galacto-configured cyclophellitol aziridine inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 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 No protein-ligand interaction detected (PLIP)

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

NAG.2: 4 residues within 4Å: Chain A: T.138, D.141, H.145, N.146 No protein-ligand interaction detected (PLIP) NAG.3: 1 residues within 4Å: Chain A: N.270 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: K.74, F.75, Q.76, H.328, H.374 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.374 Water bridges: A:H.328

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

SO4.5: 4 residues within 4Å: Chain A: K.79, W.228, R.277, H.306 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:W.228 Water bridges: A:K.79, A:R.277, A:R.277, A:H.306, A:E.429, A:E.429 Salt bridges: A:K.79, A:R.277, A:H.306 SO4.6: 6 residues within 4Å: Chain A: Y.11, S.12, R.353, S.356, W.357, D.358 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.12, A:S.12, A:S.356, A:W.357, A:D.358 Water bridges: A:R.353 Salt bridges: A:R.353 SO4.7: 3 residues within 4Å: Chain A: R.44, S.45, Y.487 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.45, A:S.45 Salt bridges: A:R.44 SO4.8: 2 residues within 4Å: Chain A: K.473, P.475 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.473, A:K.473 Salt bridges: A:K.473 SO4.9: 2 residues within 4Å: Chain A: E.254, R.257 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.254, A:E.254 Salt bridges: A:R.257 SO4.10: 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 SO4.11: 5 residues within 4Å: Chain A: Y.11, W.348, E.349, Q.350, R.353 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.11, A:Q.350 Water bridges: A:R.353 Salt bridges: A:R.353

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

EDO.12: 3 residues within 4Å: Chain A: P.289, H.290, K.293 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.290, A:K.293 Water bridges: A:H.290 EDO.13: 3 residues within 4Å: Chain A: R.170, P.428 Ligands: EDO.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.170, A:R.170 EDO.14: 3 residues within 4Å: Chain A: T.187, K.198, G.199 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.199 EDO.15: 4 residues within 4Å: Chain A: Q.143, I.204, Q.207, R.211 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.211 Water bridges: A:D.203 EDO.16: 5 residues within 4Å: Chain A: R.277, K.303, Y.304, V.305, H.306 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.277, A:K.303, A:H.306 Water bridges: A:V.305, A:H.306 EDO.17: 3 residues within 4Å: Chain A: T.252, E.254, H.255 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.252, A:T.252, A:E.254, A:H.255 Water bridges: A:T.252 EDO.18: 5 residues within 4Å: Chain A: R.285, P.319, A.320, H.365, T.369 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.285, A:A.320 Water bridges: A:H.365 EDO.19: 7 residues within 4Å: Chain A: L.65, L.67, A.438, N.442, L.444, D.445, A.446 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.442, A:N.442 Water bridges: A:A.438, A:A.438 EDO.20: 9 residues within 4Å: Chain A: P.29, F.31, K.425, F.426, P.428, H.451, L.493 Ligands: EDO.13, EDO.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.425 EDO.21: 9 residues within 4Å: Chain A: F.31, P.32, H.451, S.455, A.456, L.493, W.494, H.495 Ligands: EDO.20 4 PLIP interactions: 4 interactions with chain A Water bridges: A:T.30, A:H.451, A:S.455, A:W.494 EDO.22: 6 residues within 4Å: Chain A: Q.70, Q.73, F.75, G.435, L.436, V.437 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.436

1 x UUU: (1S,2S,3S,4S,5R,6R)-5-amino-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol(Covalent)

UUU.23: 15 residues within 4Å: Chain A: C.126, D.127, F.128, W.179, N.234, E.235, F.246, Q.284, H.311, Y.313, E.340, C.342, W.381, N.396, V.398 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.340 Hydrogen bonds: A:D.127, A:W.179, A:N.234, A:N.234, A:N.396

1 x NA: SODIUM ION(Non-functional Binders)

NA.24: 4 residues within 4Å: Chain A: G.193, K.194, S.242, G.243 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.194, A:G.243 Water bridges: A:K.194

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
BBB

Glucosylceramidase

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