SMTL ID : 6q1p.3 (2 other biounits)

Glucocerebrosidase in complex with pharmacological chaperone norIMX8

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

4 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: 4 residues within 4Å: Chain A: I.5, N.19, T.21, Y.22 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: I.5, N.19, T.21, Y.22 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 4 residues within 4Å: Chain C: I.5, N.19, T.21, Y.22 No protein-ligand interaction detected (PLIP) NAG-NAG.42: 4 residues within 4Å: Chain D: I.5, N.19, T.21, Y.22 No protein-ligand interaction detected (PLIP)

2 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.2: 2 residues within 4Å: Chain A: A.58, N.59 No protein-ligand interaction detected (PLIP) NAG-FUC.41: 2 residues within 4Å: Chain C: A.58, N.59 No protein-ligand interaction detected (PLIP)

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

EDO.4: 2 residues within 4Å: Chain A: H.290, K.293 Ligand excluded by PLIP EDO.5: 2 residues within 4Å: Chain A: E.254, R.257 Ligand excluded by PLIP EDO.6: 1 residues within 4Å: Chain A: R.277 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: T.187, K.198, G.199 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: R.285, P.319, A.320, T.369 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: D.24, S.25, F.26, R.48, Y.418 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: F.75, H.328, H.374 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: H.60, G.62, T.63, G.64, L.66 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain A: S.45, R.47 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain B: P.3, C.4, G.46, R.47, R.48, E.50 Ligands: EDO.27 Ligand excluded by PLIP EDO.23: 2 residues within 4Å: Chain B: Q.143, H.145 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain B: K.155 Chain C: R.131, P.150 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain B: L.268, A.269, H.274, V.276, Y.304 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain B: R.44, S.465, Y.487 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain B: D.24, S.25, F.26, R.48, Y.418 Ligands: EDO.22 Ligand excluded by PLIP EDO.28: 1 residues within 4Å: Chain B: R.277 Ligand excluded by PLIP EDO.43: 2 residues within 4Å: Chain C: H.290, K.293 Ligand excluded by PLIP EDO.44: 2 residues within 4Å: Chain C: E.254, R.257 Ligand excluded by PLIP EDO.45: 1 residues within 4Å: Chain C: R.277 Ligand excluded by PLIP EDO.46: 3 residues within 4Å: Chain C: T.187, K.198, G.199 Ligand excluded by PLIP EDO.47: 4 residues within 4Å: Chain C: R.285, P.319, A.320, T.369 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain C: D.24, S.25, F.26, R.48, Y.418 Ligand excluded by PLIP EDO.49: 3 residues within 4Å: Chain C: F.75, H.328, H.374 Ligand excluded by PLIP EDO.50: 5 residues within 4Å: Chain C: H.60, G.62, T.63, G.64, L.66 Ligand excluded by PLIP EDO.51: 2 residues within 4Å: Chain C: S.45, R.47 Ligand excluded by PLIP EDO.61: 7 residues within 4Å: Chain D: P.3, C.4, G.46, R.47, R.48, E.50 Ligands: EDO.66 Ligand excluded by PLIP EDO.62: 2 residues within 4Å: Chain D: Q.143, H.145 Ligand excluded by PLIP EDO.63: 3 residues within 4Å: Chain A: R.131, P.150 Chain D: K.155 Ligand excluded by PLIP EDO.64: 5 residues within 4Å: Chain D: L.268, A.269, H.274, V.276, Y.304 Ligand excluded by PLIP EDO.65: 3 residues within 4Å: Chain D: R.44, S.465, Y.487 Ligand excluded by PLIP EDO.66: 6 residues within 4Å: Chain D: D.24, S.25, F.26, R.48, Y.418 Ligands: EDO.61 Ligand excluded by PLIP EDO.67: 1 residues within 4Å: Chain D: R.277 Ligand excluded by PLIP

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

SO4.13: 6 residues within 4Å: Chain A: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain A: K.79, W.228, R.277, H.306 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain A: R.44, S.45 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain A: R.44, S.465, Y.487 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain A: R.170, P.428 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain A: A.1, R.2 Ligand excluded by PLIP SO4.29: 6 residues within 4Å: Chain B: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain B: K.79, W.228, R.277, H.306 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain B: G.193, K.194, S.242, G.243 Ligand excluded by PLIP SO4.32: 2 residues within 4Å: Chain B: R.44, S.45 Ligand excluded by PLIP SO4.33: 2 residues within 4Å: Chain B: T.187, G.199 Ligand excluded by PLIP SO4.34: 2 residues within 4Å: Chain B: R.170, P.428 Ligand excluded by PLIP SO4.35: 2 residues within 4Å: Chain B: K.321, R.329 Ligand excluded by PLIP SO4.36: 2 residues within 4Å: Chain B: S.45, R.47 Ligand excluded by PLIP SO4.37: 3 residues within 4Å: Chain B: I.158, P.159, H.162 Ligand excluded by PLIP SO4.38: 2 residues within 4Å: Chain B: H.290, K.293 Ligand excluded by PLIP SO4.52: 6 residues within 4Å: Chain C: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP SO4.53: 4 residues within 4Å: Chain C: K.79, W.228, R.277, H.306 Ligand excluded by PLIP SO4.54: 2 residues within 4Å: Chain C: R.44, S.45 Ligand excluded by PLIP SO4.55: 3 residues within 4Å: Chain C: R.44, S.465, Y.487 Ligand excluded by PLIP SO4.56: 2 residues within 4Å: Chain C: R.170, P.428 Ligand excluded by PLIP SO4.57: 2 residues within 4Å: Chain C: A.1, R.2 Ligand excluded by PLIP SO4.68: 6 residues within 4Å: Chain D: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP SO4.69: 4 residues within 4Å: Chain D: K.79, W.228, R.277, H.306 Ligand excluded by PLIP SO4.70: 4 residues within 4Å: Chain D: G.193, K.194, S.242, G.243 Ligand excluded by PLIP SO4.71: 2 residues within 4Å: Chain D: R.44, S.45 Ligand excluded by PLIP SO4.72: 2 residues within 4Å: Chain D: T.187, G.199 Ligand excluded by PLIP SO4.73: 2 residues within 4Å: Chain D: R.170, P.428 Ligand excluded by PLIP SO4.74: 2 residues within 4Å: Chain D: K.321, R.329 Ligand excluded by PLIP SO4.75: 2 residues within 4Å: Chain D: S.45, R.47 Ligand excluded by PLIP SO4.76: 3 residues within 4Å: Chain D: I.158, P.159, H.162 Ligand excluded by PLIP SO4.77: 2 residues within 4Å: Chain D: H.290, K.293 Ligand excluded by PLIP

4 x P8Y: (2S,3S,4S,5R)-2-{[(4-methylpentyl)sulfonyl]methyl}piperidine-3,4,5-triol(Non-covalent)

P8Y.19: 12 residues within 4Å: Chain A: D.127, F.128, W.179, E.235, Y.244, F.246, Q.284, Y.313, E.340, W.381, N.396 Chain B: W.348 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.244, A:F.246, A:F.246, B:W.348 Hydrogen bonds: A:D.127, A:E.235, A:Y.313, A:N.396 P8Y.39: 14 residues within 4Å: Chain A: W.348 Chain B: D.127, F.128, W.179, E.235, Y.244, P.245, F.246, Q.284, Y.313, E.340, W.381, N.396, V.398 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.244, B:P.245, B:F.246, A:W.348 Hydrogen bonds: B:D.127, B:E.235, B:N.396 Water bridges: B:N.396 P8Y.58: 12 residues within 4Å: Chain C: D.127, F.128, W.179, E.235, Y.244, F.246, Q.284, Y.313, E.340, W.381, N.396 Chain D: W.348 8 PLIP interactions: 1 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:W.348, C:Y.244, C:F.246, C:F.246 Hydrogen bonds: C:D.127, C:E.235, C:Y.313, C:N.396 P8Y.78: 14 residues within 4Å: Chain C: W.348 Chain D: D.127, F.128, W.179, E.235, Y.244, P.245, F.246, Q.284, Y.313, E.340, W.381, N.396, V.398 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.244, D:P.245, D:F.246, C:W.348 Hydrogen bonds: D:D.127, D:E.235, D:N.396 Water bridges: D:N.396

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

NAG.20: 1 residues within 4Å: Chain B: N.59 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.59 NAG.21: 5 residues within 4Å: Chain B: T.138, N.146 Chain C: L.96, S.97, P.98 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.138 NAG.59: 1 residues within 4Å: Chain D: N.59 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.59 NAG.60: 5 residues within 4Å: Chain A: L.96, S.97, P.98 Chain D: T.138, N.146 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Santana, A.G. et al., Pharmacological chaperones for GCase that switch conformation with pH enhance enzyme levels in Gaucher animal models. To Be Published

Release Date

2020-08-19

Peptides

Glucosylceramidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Glucosylceramidase

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