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

Structure of recombinant human beta-glucocerebrosidase in complex with N-acyl functionalised cyclophellitol aziridine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 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

2 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) NAG.3: 1 residues within 4Å: Chain A: N.270 No protein-ligand interaction detected (PLIP)

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

SO4.4: 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 SO4.5: 4 residues within 4Å: Chain A: K.79, W.228, R.277, H.306 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.228 Water bridges: A:H.306, A:H.306, A:E.429 Salt bridges: A:K.79, A:R.277, A:H.306 SO4.6: 2 residues within 4Å: Chain A: K.321, R.329 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.326 Salt bridges: A:K.321, A:R.329 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:R.44, A:G.486 Salt bridges: A:R.44 SO4.8: 5 residues within 4Å: Chain A: N.188, G.193, K.194, S.242, G.243 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.194, A:G.243 Water bridges: A:N.188, A:N.192 SO4.9: 3 residues within 4Å: Chain A: R.44, S.465, Y.487 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.487 Salt bridges: A:R.44

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

EDO.10: 9 residues within 4Å: Chain A: G.265, L.268, A.269, H.274, V.276, R.277, L.278, Y.304 Ligands: EDO.11 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.278 EDO.11: 6 residues within 4Å: Chain A: R.277, K.303, Y.304, V.305, H.306 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.306 Water bridges: A:H.306 EDO.12: 4 residues within 4Å: Chain A: D.27, P.28, P.29, T.30 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.28 Water bridges: A:D.27, A:T.30 EDO.13: 3 residues within 4Å: Chain A: R.131, T.132, Y.133 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.131, A:T.132, A:T.132 EDO.14: 6 residues within 4Å: Chain A: T.154, K.155, I.158, P.159, H.162, H.223 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.154, A:H.223, A:H.223 EDO.15: 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.16: 2 residues within 4Å: Chain A: E.254, R.257 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.257, A:R.257 Water bridges: A:E.254 EDO.17: 6 residues within 4Å: Chain A: D.453, G.454, S.455, H.495, R.496, Q.497 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.496, A:Q.497, A:Q.497 EDO.18: 1 residues within 4Å: Chain A: K.155 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.155

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.19: 8 residues within 4Å: Chain A: P.3, C.4, P.6, G.46, R.47, R.48, E.50 Ligands: GOL.20 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:C.4, A:G.46, A:G.46, A:R.48 Water bridges: A:R.47 GOL.20: 12 residues within 4Å: Chain A: R.2, P.3, C.4, D.24, S.25, F.26, R.48, M.49, E.50, K.413, Y.418 Ligands: GOL.19 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:C.4, A:D.24, A:D.24, A:M.49 Water bridges: A:K.413 GOL.21: 3 residues within 4Å: Chain A: I.204, Q.207, R.211 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.211, A:R.211

1 x K35: ~{N}-[(1~{R},2~{R},3~{R},4~{S},5~{S},6~{S})-2-(hydroxymethyl)-3,4,5,6-tetrakis(oxidanyl)cyclohexyl]pentanamide(Covalent)

K35.22: 18 residues within 4Å: Chain A: C.126, D.127, F.128, W.179, N.234, E.235, Y.244, F.246, Q.284, H.311, Y.313, L.314, E.340, C.342, W.381, N.392, N.396, V.398 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.313, A:E.340 Hydrogen bonds: A:D.127, A:W.179, A:N.234, A:E.235, A:Q.284, 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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