SMTL ID : 6ytr.1 (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- 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: 7 residues within 4Å: Chain A: R.2, I.5, N.19, A.20, T.21, Y.22 Ligands: EDO.26 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.22

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)

PO8.2: 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 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:E.235, A:S.345, A:W.381, A:N.396

4 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.12, A:S.12, A:W.357, A:D.358 Water bridges: A:R.353, A:R.359 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:K.79, A:H.306 Salt bridges: A:K.79, A:R.277, A:H.306 SO4.11: 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 SO4.22: 5 residues within 4Å: Chain A: L.296, F.331, P.332, N.333, T.334 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.333, A:T.334, A:T.334

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

NAG.5: 3 residues within 4Å: Chain A: T.138, H.145, N.146 No protein-ligand interaction detected (PLIP)

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

EDO.6: 3 residues within 4Å: Chain A: R.44, S.45, Y.487 Ligand excluded by PLIP EDO.7: 10 residues within 4Å: Chain A: R.285, V.310, H.311, W.312, D.315, L.324, A.338, S.366, N.370, W.378 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: R.285, D.315, F.316, A.320, H.365, S.366, T.369 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: W.348, E.349, Q.350, R.353, R.359 Ligand excluded by PLIP EDO.10: 10 residues within 4Å: Chain A: R.2, C.4, D.24, S.25, F.26, R.48, M.49, K.413, F.417, Y.418 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: R.39, S.52, M.53, G.54 Ligands: EDO.13 Ligand excluded by PLIP EDO.13: 10 residues within 4Å: Chain A: R.39, E.41, R.47, S.52, T.482, I.483, P.485, H.490, Y.492 Ligands: EDO.12 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: R.277, A.302, K.303, Y.304, V.305, H.306 Ligands: EDO.15 Ligand excluded by PLIP EDO.15: 8 residues within 4Å: Chain A: H.274, N.275, V.276, R.277, L.278, H.306 Ligands: EDO.14, EDO.17 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: L.165, A.168, Q.169, R.170, P.171, V.172 Ligand excluded by PLIP EDO.17: 8 residues within 4Å: Chain A: G.265, L.268, A.269, H.274, V.276, L.278, Y.304 Ligands: EDO.15 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain A: E.254, R.257 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain A: G.193, K.194, S.242, G.243, Y.244 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain A: S.196, G.199, Q.200, P.201, H.206, H.255 Ligand excluded by PLIP EDO.21: 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.24: 6 residues within 4Å: Chain A: F.9, L.354, P.387, D.405, K.408, Y.412 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain A: A.261, R.262, P.266, E.300, K.303, Y.304 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain A: V.17, N.19, K.408, T.410 Ligands: NAG-NAG-BMA-MAN.1 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain A: D.358, M.361, Q.362, H.365, R.463 Ligand excluded by PLIP

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

NA.23: 4 residues within 4Å: Chain A: G.344, K.346, F.347, E.349 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.346, A:E.349

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
AAA

Lysosomal acid glucosylceramidase

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