SMTL ID : 6z39.1

Structure of recombinant human beta-glucocerebrosidase in complex with BODIPY functionalised epoxide activity based probe

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.138 NAG.25: 3 residues within 4Å: Chain B: T.138, H.145, N.146 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.138

1 x Q65: (1~{S},2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[4-[4-[(12~{R})-2,2-bis(fluoranyl)-4,6,10,12-tetramethyl-1,3-diaza-2$l^{4}-boratricyclo[7.3.0.0^{3,7}]dodeca-4,6,9-trien-8-yl]butyl]-1,2,3-triazol-1-yl]methyl]-7-oxabicyclo[4.1.0]heptane-2,3,4-triol(Non-covalent)

Q65.4: 17 residues within 4Å: Chain A: S.237, L.240, L.241, S.242, G.243, Y.244, P.245, F.246, L.286, L.287, V.394, N.396 Chain B: F.316, F.347, W.348 Ligands: K35.5, GAI.24 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.241, A:Y.244, A:P.245, A:N.396, B:F.347, B:W.348, B:W.348, B:W.348 Hydrogen bonds: A:S.237

2 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)

K35.5: 22 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, F.316, E.340, C.342, W.381, N.392, N.396, V.398 Chain B: F.347, W.348 Ligands: Q65.4, GAI.24 12 PLIP interactions: 12 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 Water bridges: A:E.235, A:Y.244, A:N.396 K35.27: 21 residues within 4Å: Chain A: K.346 Chain B: 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, S.345, K.346, W.381, N.392, N.396, V.398 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.313, B:Y.313, B:E.340 Hydrogen bonds: B:D.127, B:W.179, B:N.234, B:E.235, B:E.235, B:S.345, B:W.381 Water bridges: B:N.396, B:N.396

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

SO4.6: 7 residues within 4Å: Chain A: Y.11, S.12, R.353, S.356, W.357, D.358 Chain B: S.242 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.12, A:S.12, A:S.356, A:W.357, A:D.358 Water bridges: A:R.353, A:R.353, A:S.356 Salt bridges: A:R.353 SO4.7: 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 SO4.8: 2 residues within 4Å: Chain A: K.321, R.329 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.321, A:R.329 SO4.9: 3 residues within 4Å: Chain A: R.44, S.45, Y.487 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.44, A:S.45, A:G.486 Salt bridges: A:R.44 SO4.10: 6 residues within 4Å: Chain A: N.188, G.193, K.194, S.242, G.243, Y.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.194, A:G.243 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 SO4.28: 4 residues within 4Å: Chain B: K.79, W.228, R.277, H.306 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:W.228 Water bridges: B:K.79, B:H.306 Salt bridges: B:K.79, B:R.277, B:H.306 SO4.29: 6 residues within 4Å: Chain B: Y.11, S.12, R.353, S.356, W.357, D.358 10 PLIP interactions: 10 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:R.353, B:R.359 Salt bridges: B:R.353 SO4.30: 3 residues within 4Å: Chain B: R.44, S.45, Y.487 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.45 Water bridges: B:R.44, B:S.45 Salt bridges: B:R.44 SO4.31: 3 residues within 4Å: Chain B: K.473, P.475 Ligands: GOL.44 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.473, B:K.473 Salt bridges: B:K.473 SO4.32: 2 residues within 4Å: Chain B: E.254, R.257 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.254, B:E.254 Salt bridges: B:R.257 SO4.33: 3 residues within 4Å: Chain B: R.44, S.465, Y.487 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.44 SO4.34: 1 residues within 4Å: Chain B: R.277 2 PLIP interactions: 2 interactions with chain B Water bridges: B:H.306 Salt bridges: B:R.277

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

EDO.12: 7 residues within 4Å: Chain A: G.265, L.268, A.269, H.274, V.276, L.278, Y.304 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: R.170, P.428 Ligands: EDO.19 Ligand excluded by PLIP EDO.14: 9 residues within 4Å: Chain A: Y.133, T.134, Y.135, A.136, D.137, T.138, N.146, F.147, S.148 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: T.154, I.158, P.159, H.162, H.223 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: T.187, K.198, G.199 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: L.165, A.168, R.170, P.171, V.172 Ligand excluded by PLIP EDO.18: 1 residues within 4Å: Chain A: R.262 Ligand excluded by PLIP EDO.19: 9 residues within 4Å: Chain A: P.29, Y.40, R.170, K.425, F.426, P.428, H.451, L.493 Ligands: EDO.13 Ligand excluded by PLIP EDO.20: 8 residues within 4Å: Chain A: L.67, L.436, V.437, A.438, N.442, L.444, D.445, A.446 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain A: D.27, P.28, P.29, T.30 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain B: P.289, H.290, K.293 Ligand excluded by PLIP EDO.36: 8 residues within 4Å: Chain B: G.265, L.268, A.269, H.274, V.276, R.277, L.278, Y.304 Ligand excluded by PLIP EDO.37: 8 residues within 4Å: Chain B: F.31, P.32, F.37, S.38, S.455, L.493, W.494, H.495 Ligand excluded by PLIP EDO.38: 2 residues within 4Å: Chain B: P.469, I.483 Ligand excluded by PLIP EDO.39: 5 residues within 4Å: Chain B: D.358, M.361, Q.362, H.365, R.463 Ligand excluded by PLIP EDO.40: 6 residues within 4Å: Chain B: L.67, A.438, N.442, L.444, D.445, A.446 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.22: 8 residues within 4Å: Chain A: P.3, C.4, P.6, G.46, R.47, R.48, E.50 Ligands: GOL.23 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.4, A:C.4, A:G.46, A:R.48 GOL.23: 13 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, F.417, Y.418 Ligands: GOL.22 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.24, A:R.48, A:R.48 Water bridges: A:D.24, A:D.24 GOL.41: 11 residues within 4Å: Chain B: R.2, P.3, C.4, D.24, S.25, F.26, R.48, M.49, E.50, K.413, Y.418 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:C.4, B:D.24, B:D.24, B:D.24 Water bridges: B:M.49, B:L.51, B:K.413 GOL.42: 6 residues within 4Å: Chain B: E.349, Q.350, S.351, V.352, R.395, F.397 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.351, B:S.351, B:S.351, B:S.351, B:R.395, B:R.395 GOL.43: 4 residues within 4Å: Chain B: R.131, Y.133, P.150, E.151 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.131, B:R.131, B:E.151 GOL.44: 8 residues within 4Å: Chain B: A.58, K.473, D.474, P.475, V.477, G.478, F.479 Ligands: SO4.31 2 PLIP interactions: 2 interactions with chain B Water bridges: B:P.475, B:A.476

1 x GAI: GUANIDINE(Non-covalent)

GAI.24: 10 residues within 4Å: Chain A: E.235, S.237, A.238, L.241, Y.244, D.283, Q.284, L.287 Ligands: Q65.4, K35.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.237, A:S.237, A:S.237 Water bridges: A:E.235, A:Y.244 Salt bridges: A:E.235, A:D.283

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.26: 2 residues within 4Å: Chain B: R.170, P.428 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.428 Salt bridges: B:R.170

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

Glucosylceramidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

Glucosylceramidase

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