SMTL ID : 7nwv.1

Structure of recombinant human beta-glucocerebrosidase in complex with BODIPY Tagged Cyclophellitol activity based probe

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- AH2: 1-deoxy-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-AH2.1: 6 residues within 4Å: Chain A: R.2, I.5, N.19, A.20, T.21, Y.22 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.22 NAG-NAG-AH2.2: 5 residues within 4Å: Chain B: I.5, N.19, A.20, T.21, Y.22 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.5

8 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 8 PLIP interactions: 8 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.353, A:R.359 Salt bridges: A:R.353 SO4.5: 5 residues within 4Å: Chain A: K.79, W.228, R.277, H.306 Ligands: EDO.8 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.228 Water bridges: A:K.79, A:K.79, A:H.306 Salt bridges: A:K.79, A:R.277, A:H.306 SO4.12: 5 residues within 4Å: Chain A: 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 SO4.32: 6 residues within 4Å: Chain B: Y.11, S.12, R.353, S.356, W.357, D.358 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.12, B:S.12, B:S.356, B:W.357, B:D.358 Water bridges: B:R.353, B:R.353, B:D.358 Salt bridges: B:R.353 SO4.34: 4 residues within 4Å: Chain B: K.79, W.228, R.277, H.306 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:W.228 Water bridges: B:K.79, B:K.79, B:K.79, B:R.277, B:R.277, B:H.306, B:H.306 Salt bridges: B:K.79, B:R.277, B:H.306 SO4.44: 8 residues within 4Å: Chain B: G.265, L.268, A.269, H.274, V.276, R.277, L.278, Y.304 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.274, B:L.278, B:Y.304 SO4.47: 4 residues within 4Å: Chain B: G.193, K.194, S.242, G.243 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.194, B:G.243 SO4.48: 3 residues within 4Å: Chain B: R.44, S.465, Y.487 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.487 Salt bridges: B:R.44

2 x UUH: (1~{S},2~{R},3~{R},4~{S},5~{S})-4-[[4-[4-[2,2-bis(fluoranyl)-4,6,10,12-tetramethyl-3-aza-1-azonia-2-boranuidatricyclo[7.3.0.0^{3,7}]dodeca-1(12),4,6,8,10-pentaen-8-yl]butyl]-1,2,3-triazol-1-yl]methyl]cyclohexane-1,2,3,5-tetrol(Covalent)

UUH.4: 30 residues within 4Å: Chain A: R.120, D.127, F.128, W.179, N.234, E.235, L.241, Y.244, F.246, H.311, Y.313, L.314, F.316, E.340, C.342, S.345, K.346, W.348, W.381, N.396, V.398 Chain B: L.241, Y.244, Y.313, L.314, F.316, W.348 Ligands: EDO.19, UUH.33, EDO.51 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.241, A:Y.313, A:L.314, A:F.316, A:E.340, B:L.241, B:L.314 Hydrogen bonds: A:D.127, A:W.179, A:N.234, A:E.340, A:W.381, A:N.396 pi-Stacking: A:Y.313 UUH.33: 18 residues within 4Å: Chain B: R.120, C.126, D.127, F.128, W.179, N.234, E.235, F.246, H.311, Y.313, E.340, C.342, S.345, W.381, N.396, V.398 Ligands: UUH.4, EDO.51 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.313, B:E.340 Hydrogen bonds: B:D.127, B:W.179, B:N.234, B:E.340, B:W.381, B:N.396 Water bridges: B:E.235

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

NAG.6: 3 residues within 4Å: Chain A: T.138, H.145, N.146 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.138 NAG.35: 3 residues within 4Å: Chain B: T.138, H.145, N.146 No protein-ligand interaction detected (PLIP) NAG.45: 3 residues within 4Å: Chain B: N.270, S.271, T.272 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.270 Water bridges: B:N.270

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

EDO.7: 11 residues within 4Å: Chain A: R.2, P.3, C.4, D.24, S.25, F.26, R.48, M.49, G.113, K.413, Y.418 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: K.77, K.79, H.306, M.335, V.376 Ligands: SO4.5 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: F.75, L.372, Y.373, H.374, R.433 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: L.165, A.168, R.170, P.171, V.172 Ligands: UUE.26 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: R.44, S.45, Y.487 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: T.183, W.184, K.186, G.189, K.198 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: T.187, K.198, G.199, Y.205 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: E.254, R.257 Ligands: EDO.28 Ligand excluded by PLIP EDO.16: 9 residues within 4Å: Chain A: G.265, L.268, A.269, H.274, V.276, R.277, L.278, Y.304 Ligands: EDO.17 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: R.277, A.302, K.303, Y.304, V.305, H.306 Ligands: EDO.16 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain A: R.131, Y.133, T.134, Y.135, D.137, P.150 Ligand excluded by PLIP EDO.19: 9 residues within 4Å: Chain A: E.235, S.237, A.238, Y.244, D.283, Q.284 Chain B: F.316, L.317 Ligands: UUH.4 Ligand excluded by PLIP EDO.20: 11 residues within 4Å: Chain A: L.286, L.287, H.290, W.291 Chain B: L.286, L.317, A.318, P.319, A.322, T.323 Ligands: EDO.21 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain A: L.286, L.287, L.288, P.289, H.290, K.293 Chain B: P.289 Ligands: EDO.20 Ligand excluded by PLIP EDO.22: 12 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 Ligands: EDO.23 Ligand excluded by PLIP EDO.23: 8 residues within 4Å: Chain A: R.285, W.312, D.315, H.365, S.366, T.369, N.370 Ligands: EDO.22 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain A: L.91, N.92, A.95, N.386, P.391, I.406 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain A: A.476, V.477, R.496, Q.497 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain A: A.261, R.262, P.266, E.300, K.303, Y.304 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain A: T.252, E.254, H.255 Ligands: EDO.15, EDO.29 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain A: S.196, G.199, Q.200, P.201, H.255 Ligands: EDO.28 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain A: N.270, S.271, T.272 Ligand excluded by PLIP EDO.31: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.36: 8 residues within 4Å: Chain B: P.3, C.4, D.24, G.46, R.47, R.48, E.50 Ligands: EDO.37 Ligand excluded by PLIP EDO.37: 11 residues within 4Å: Chain B: R.2, P.3, C.4, D.24, S.25, F.26, R.48, M.49, K.413, Y.418 Ligands: EDO.36 Ligand excluded by PLIP EDO.38: 2 residues within 4Å: Chain B: K.106, L.167 Ligand excluded by PLIP EDO.39: 7 residues within 4Å: Chain B: L.91, N.92, A.95, N.386, P.391, V.404, I.406 Ligand excluded by PLIP EDO.40: 4 residues within 4Å: Chain B: S.12, R.44, S.45, Y.487 Ligand excluded by PLIP EDO.41: 8 residues within 4Å: Chain B: R.39, E.41, R.47, S.52, T.482, I.483, P.485, H.490 Ligand excluded by PLIP EDO.42: 7 residues within 4Å: Chain B: F.31, P.32, S.38, S.455, L.493, W.494, R.495 Ligand excluded by PLIP EDO.43: 6 residues within 4Å: Chain B: D.453, G.454, S.455, R.495, R.496, Q.497 Ligand excluded by PLIP EDO.46: 3 residues within 4Å: Chain B: L.94, P.98, Q.101 Ligand excluded by PLIP EDO.49: 2 residues within 4Å: Chain B: E.254, R.257 Ligand excluded by PLIP EDO.50: 5 residues within 4Å: Chain B: L.296, F.331, P.332, N.333, T.334 Ligand excluded by PLIP EDO.51: 6 residues within 4Å: Chain A: W.348 Chain B: K.346, F.347, W.348 Ligands: UUH.4, UUH.33 Ligand excluded by PLIP

1 x UUE: 8-[4-(1-ethyl-1,2,3-triazol-4-yl)butyl]-2,2-bis(fluoranyl)-4,6,10,12-tetramethyl-3-aza-1-azonia-2-boranuidatricyclo[7.3.0.0^{3,7}]dodeca-1(12),4,6,8,10-pentaene(Non-covalent)

UUE.26: 10 residues within 4Å: Chain A: I.158, P.159, H.162, R.163, L.165, Q.166, H.223, K.224, L.225 Ligands: EDO.10 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.159, A:R.163, A:L.165, A:Q.166, A:K.224 Hydrogen bonds: A:H.162 pi-Stacking: A:H.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van der Gracht, D. et al., Fluorescence polarisation activity-based protein profiling for the identification of deoxynojirimycin-type inhibitors selective for lysosomal retaining alpha- and beta-glucosidases. Chem Sci (2023)

Release Date

2022-03-30

Peptides

Lysosomal acid glucosylceramidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

Lysosomal acid glucosylceramidase

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