SMTL ID : 6z3i.1

Structure of recombinant beta-glucocerebrosidase in complex with bifunctional cyclophellitol aziridine activity based probe

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 5 residues within 4Å: Chain A: I.5, N.19, A.20, T.21, Y.22 No protein-ligand interaction detected (PLIP)

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

SO4.2: 6 residues within 4Å: Chain A: Y.11, S.12, R.353, S.356, W.357, D.358 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.12, A:S.12, A:W.357, A:D.358 Water bridges: A:R.44, A:R.353, A:R.353, A:R.353, A:S.356 Salt bridges: A:R.353 SO4.4: 4 residues within 4Å: Chain A: K.79, W.228, R.277, H.306 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:W.228 Water bridges: A:K.79, A:K.79, A:H.306, A:H.306 Salt bridges: A:K.79, A:R.277, A:H.306 SO4.5: 4 residues within 4Å: Chain A: F.331, P.332, N.333, T.334 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.333, A:N.333, A:T.334 SO4.8: 6 residues within 4Å: Chain A: N.188, G.193, K.194, S.242, G.243, Y.244 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.194, A:G.243 Water bridges: A:K.194

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

NAG.3: 3 residues within 4Å: Chain A: T.138, H.145, N.146 No protein-ligand interaction detected (PLIP) NAG.16: 2 residues within 4Å: Chain A: A.58, N.59 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.59

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

EDO.6: 12 residues within 4Å: Chain A: R.2, C.23, D.24, S.25, F.26, L.103, K.106, S.107, S.110, E.112, G.113, K.413 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: P.3, C.4, G.46, R.47, R.48, E.50 Ligand excluded by PLIP EDO.9: 2 residues within 4Å: Chain A: E.254, R.257 Ligand excluded by PLIP EDO.10: 8 residues within 4Å: Chain A: G.265, L.268, A.269, H.274, V.276, R.277, L.278, Y.304 Ligand excluded by PLIP EDO.11: 11 residues within 4Å: Chain A: R.285, V.310, H.311, W.312, D.315, L.324, A.338, S.366, N.370, V.375, W.378 Ligand excluded by PLIP EDO.12: 9 residues within 4Å: Chain A: G.344, S.345, K.346, F.347, E.349, Q.350, S.351, F.397, V.398 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: R.277, K.303, Y.304, V.305, H.306 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: L.165, V.172, S.173, L.174, K.224, L.225, Q.226 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: N.386, P.387, E.388 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: R.44, S.45, Y.487 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: P.245, V.394, N.396 Ligands: Q68.17 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: I.130, R.131, T.132, W.393 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: L.69, Q.70, P.71, E.72, Q.73 Ligand excluded by PLIP EDO.22: 8 residues within 4Å: Chain A: E.235, S.237, A.238, L.241, Y.244, D.283, Q.284 Ligands: Q68.17 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain A: L.288, P.289, H.290, K.293 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain A: F.75, L.372, Y.373, H.374, R.433 Ligand excluded by PLIP

1 x Q68: ~{N}-[[1-[[(1~{S},2~{R},3~{R},4~{S},6~{S})-6-(hexylamino)-2,3,4-tris(oxidanyl)cyclohexyl]methyl]-1,2,3-triazol-4-yl]methyl]ethanamide(Covalent)

Q68.17: 22 residues within 4Å: Chain A: C.126, D.127, F.128, W.179, N.234, E.235, Y.244, P.245, F.246, Q.284, H.311, Y.313, L.314, E.340, C.342, S.345, W.381, N.392, N.396, V.398 Ligands: EDO.19, EDO.22 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:W.381, A:N.396 Water bridges: A:S.345, A:S.345

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

2021-06-30

Peptides

Lysosomal acid glucosylceramidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
BBB

Lysosomal acid glucosylceramidase

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