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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

NAG-NAG-BMA.1: 4 residues within 4Å: Chain A: I.5, N.19, T.21, Y.22 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.5

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.2: 1 residues within 4Å: Chain A: N.59 No protein-ligand interaction detected (PLIP)

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

EDO.3: 4 residues within 4Å: Chain A: L.286, L.287, H.290, W.291 Ligand excluded by PLIP EDO.7: 2 residues within 4Å: Chain A: E.254, R.257 Ligand excluded by PLIP EDO.8: 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.9: 5 residues within 4Å: Chain A: D.358, M.361, Q.362, H.365, R.463 Ligand excluded by PLIP EDO.10: 9 residues within 4Å: Chain A: C.23, D.24, S.25, L.103, K.106, S.107, S.110, E.112, K.413 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: N.102, L.105, R.163, Q.166, L.167 Ligand excluded by PLIP EDO.12: 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.13: 6 residues within 4Å: Chain A: R.277, A.302, 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: 4 residues within 4Å: Chain A: T.132, V.191, N.192, W.393 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: W.348, E.349, Q.350, R.353, R.359 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: S.45, G.46, R.47, E.50 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: R.44, S.45, Y.487 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain A: R.39, E.41, R.47, T.482, I.483, P.485, H.490, Y.492 Ligand excluded by PLIP EDO.20: 10 residues within 4Å: Chain A: R.2, P.3, C.4, D.24, S.25, F.26, R.48, M.49, K.413, Y.418 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: L.65, Q.440, K.441, N.442, D.443, V.468 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain A: T.68, L.69, Q.70, P.71, V.437, P.475 Ligand excluded by PLIP EDO.25: 1 residues within 4Å: Chain A: H.145 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain A: I.158, H.162, H.223, K.224 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain A: R.44, S.465, Y.487 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain A: E.235, S.237, A.238, Y.244, D.283, Q.284, L.314 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain A: Q.350, S.351, V.352, P.387, E.388 Ligands: EDO.30 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain A: P.387, E.388 Ligands: EDO.29 Ligand excluded by PLIP

1 x PO8: (1~{R},2~{S},3~{S},4~{S},5~{R},6~{R})-5-azanyl-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol(Covalent)

PO8.4: 17 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, S.345, W.381, N.392, N.396, V.398 11 PLIP interactions: 11 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:E.235, A:S.345, A:W.381, A:N.396 Water bridges: A:E.235

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

SO4.5: 6 residues within 4Å: Chain A: Y.11, S.12, R.353, S.356, W.357, D.358 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.12, A:S.12, A:S.356, A:W.357, A:D.358 Water bridges: A:S.12, A:R.359 Salt bridges: A:R.353 SO4.6: 4 residues within 4Å: Chain A: K.79, W.228, R.277, H.306 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.228 Water bridges: A:K.79, A:H.306 Salt bridges: A:K.79, A:R.277, A:H.306 SO4.23: 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:N.188, A:K.194, A:G.243

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

NA.24: 4 residues within 4Å: Chain A: L.165, Q.166, A.168, Q.169 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.166

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

Lysosomal acid glucosylceramidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
BBB

Lysosomal acid glucosylceramidase

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