SMTL ID : 3gxf.2 (1 other biounit)

Crystal structure of acid-beta-glucosidase with isofagomine at neutral pH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

64 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 6 residues within 4Å: Chain A: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP PO4.2: 4 residues within 4Å: Chain A: T.63, G.64, Q.440 Chain C: K.473 Ligand excluded by PLIP PO4.3: 4 residues within 4Å: Chain A: K.79, W.228, R.277, H.306 Ligand excluded by PLIP PO4.4: 2 residues within 4Å: Chain A: R.44, S.45 Ligand excluded by PLIP PO4.5: 3 residues within 4Å: Chain A: R.44, S.465, Y.487 Ligand excluded by PLIP PO4.6: 5 residues within 4Å: Chain A: Q.226, T.272, H.273, N.275, V.276 Ligand excluded by PLIP PO4.7: 4 residues within 4Å: Chain A: F.75, H.328, H.374 Chain D: K.293 Ligand excluded by PLIP PO4.8: 4 residues within 4Å: Chain A: L.165, R.170, P.171, V.172 Ligand excluded by PLIP PO4.9: 2 residues within 4Å: Chain A: H.290, K.293 Ligand excluded by PLIP PO4.10: 3 residues within 4Å: Chain A: E.72 Chain D: E.254, R.257 Ligand excluded by PLIP PO4.11: 2 residues within 4Å: Chain A: G.54, P.55 Ligand excluded by PLIP PO4.12: 5 residues within 4Å: Chain A: E.111, G.115, Q.169, R.170 Ligands: PO4.18 Ligand excluded by PLIP PO4.13: 3 residues within 4Å: Chain A: R.277, V.305, H.306 Ligand excluded by PLIP PO4.14: 2 residues within 4Å: Chain A: E.254, R.257 Ligand excluded by PLIP PO4.15: 4 residues within 4Å: Chain A: R.329, L.330 Chain D: K.321, R.329 Ligand excluded by PLIP PO4.16: 4 residues within 4Å: Chain A: T.187, L.197, K.198, G.199 Ligand excluded by PLIP PO4.17: 5 residues within 4Å: Chain A: Y.11, W.348, E.349, Q.350, R.353 Ligand excluded by PLIP PO4.18: 3 residues within 4Å: Chain A: R.170, P.428 Ligands: PO4.12 Ligand excluded by PLIP PO4.22: 6 residues within 4Å: Chain B: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP PO4.23: 4 residues within 4Å: Chain B: G.193, K.194, S.242, G.243 Ligand excluded by PLIP PO4.24: 4 residues within 4Å: Chain B: K.79, W.228, R.277, H.306 Ligand excluded by PLIP PO4.25: 2 residues within 4Å: Chain B: R.44, S.45 Ligand excluded by PLIP PO4.26: 4 residues within 4Å: Chain B: Q.226, T.272, H.273, V.276 Ligand excluded by PLIP PO4.27: 4 residues within 4Å: Chain B: T.187, K.194, G.195, S.196 Ligand excluded by PLIP PO4.28: 3 residues within 4Å: Chain B: T.187, K.198, G.199 Ligand excluded by PLIP PO4.29: 2 residues within 4Å: Chain B: H.290, K.293 Ligand excluded by PLIP PO4.30: 5 residues within 4Å: Chain B: L.330, F.331, P.332, N.333, T.334 Ligand excluded by PLIP PO4.31: 4 residues within 4Å: Chain B: R.277, K.303, V.305, H.306 Ligand excluded by PLIP PO4.32: 1 residues within 4Å: Chain B: R.262 Ligand excluded by PLIP PO4.33: 3 residues within 4Å: Chain B: L.165, P.171, V.172 Ligand excluded by PLIP PO4.34: 2 residues within 4Å: Chain B: Q.207, R.211 Ligand excluded by PLIP PO4.35: 2 residues within 4Å: Chain B: Q.143, H.145 Ligand excluded by PLIP PO4.36: 5 residues within 4Å: Chain B: V.214, D.218, S.271, T.272, H.273 Ligand excluded by PLIP PO4.37: 4 residues within 4Å: Chain B: K.321, R.329 Chain C: R.329, L.330 Ligand excluded by PLIP PO4.38: 3 residues within 4Å: Chain B: R.44, S.465, Y.487 Ligand excluded by PLIP PO4.39: 3 residues within 4Å: Chain B: I.158, P.159, H.162 Ligand excluded by PLIP PO4.44: 6 residues within 4Å: Chain C: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP PO4.45: 5 residues within 4Å: Chain A: K.473 Chain C: T.63, G.64, L.65, Q.440 Ligand excluded by PLIP PO4.46: 2 residues within 4Å: Chain C: R.44, S.45 Ligand excluded by PLIP PO4.47: 4 residues within 4Å: Chain C: K.79, W.228, R.277, H.306 Ligand excluded by PLIP PO4.48: 7 residues within 4Å: Chain C: Q.226, F.227, T.272, H.273, H.274, N.275, V.276 Ligand excluded by PLIP PO4.49: 5 residues within 4Å: Chain C: Y.11, W.348, E.349, Q.350, R.353 Ligand excluded by PLIP PO4.50: 4 residues within 4Å: Chain C: E.111, Q.169, R.170, P.428 Ligand excluded by PLIP PO4.51: 3 residues within 4Å: Chain C: S.465, K.466, D.467 Ligand excluded by PLIP PO4.52: 5 residues within 4Å: Chain C: T.154, I.158, P.159, H.162, H.223 Ligand excluded by PLIP PO4.53: 2 residues within 4Å: Chain C: E.254, R.257 Ligand excluded by PLIP PO4.54: 4 residues within 4Å: Chain C: R.277, K.303, V.305, H.306 Ligand excluded by PLIP PO4.55: 3 residues within 4Å: Chain C: R.44, S.465, Y.487 Ligand excluded by PLIP PO4.56: 3 residues within 4Å: Chain C: F.75, H.328, H.374 Ligand excluded by PLIP PO4.57: 4 residues within 4Å: Chain C: L.165, R.170, P.171, V.172 Ligand excluded by PLIP PO4.58: 2 residues within 4Å: Chain C: H.290, K.293 Ligand excluded by PLIP PO4.61: 7 residues within 4Å: Chain C: S.242 Chain D: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP PO4.62: 4 residues within 4Å: Chain D: G.193, K.194, S.242, G.243 Ligand excluded by PLIP PO4.63: 4 residues within 4Å: Chain D: K.79, W.228, R.277, H.306 Ligand excluded by PLIP PO4.64: 4 residues within 4Å: Chain D: Q.226, T.272, H.273, V.276 Ligand excluded by PLIP PO4.65: 2 residues within 4Å: Chain D: R.44, S.45 Ligand excluded by PLIP PO4.66: 5 residues within 4Å: Chain D: T.154, I.158, P.159, H.162, H.223 Ligand excluded by PLIP PO4.67: 2 residues within 4Å: Chain D: H.290, K.293 Ligand excluded by PLIP PO4.68: 3 residues within 4Å: Chain D: T.187, K.198, G.199 Ligand excluded by PLIP PO4.69: 2 residues within 4Å: Chain D: Q.207, R.211 Ligand excluded by PLIP PO4.70: 3 residues within 4Å: Chain D: R.44, S.465, Y.487 Ligand excluded by PLIP PO4.71: 3 residues within 4Å: Chain D: L.165, P.171, V.172 Ligand excluded by PLIP PO4.72: 3 residues within 4Å: Chain D: R.277, V.305, H.306 Ligand excluded by PLIP PO4.73: 4 residues within 4Å: Chain D: L.67, A.438, N.442, L.444 Ligand excluded by PLIP

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

NAG.19: 4 residues within 4Å: Chain A: I.5, N.19, T.21, Y.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.19 Water bridges: A:T.21 NAG.40: 4 residues within 4Å: Chain B: I.5, N.19, T.21, Y.22 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.19, B:T.21 NAG.59: 3 residues within 4Å: Chain C: I.5, N.19, Y.22 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.19 Water bridges: C:N.19, C:T.21 NAG.74: 4 residues within 4Å: Chain D: I.5, N.19, T.21, Y.22 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.19, D:T.21

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.20: 8 residues within 4Å: Chain A: D.127, F.128, W.179, N.234, E.235, E.340, W.381, F.397 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.127, A:N.234, A:E.235 GOL.21: 6 residues within 4Å: Chain A: R.2, D.24, S.25, F.26, R.48, M.49 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.24, A:D.24 Water bridges: A:C.4, A:K.413 GOL.42: 10 residues within 4Å: Chain B: R.2, P.3, C.4, D.24, S.25, F.26, R.48, M.49, Y.418 Ligands: GOL.43 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.2, B:C.4 Water bridges: B:K.413 GOL.43: 6 residues within 4Å: Chain B: F.26, Y.40, M.49, E.50, L.51 Ligands: GOL.42 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.51 GOL.60: 7 residues within 4Å: Chain C: D.127, F.128, W.179, E.235, E.340, W.381, F.397 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:W.179, C:E.235 Water bridges: C:N.234

2 x IFM: 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE(Non-covalent)

IFM.41: 12 residues within 4Å: Chain B: D.127, F.128, W.179, N.234, E.235, F.246, Y.313, E.340, C.342, S.345, W.381, N.396 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.127, B:D.127, B:E.340, B:S.345, B:N.396 Water bridges: B:Q.284 IFM.75: 11 residues within 4Å: Chain D: D.127, F.128, W.179, N.234, E.235, F.246, Y.313, E.340, C.342, W.381, N.396 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.127, D:D.127, D:E.235, D:N.396, D:N.396

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lieberman, R.L. et al., Effects of pH and iminosugar pharmacological chaperones on lysosomal glycosidase structure and stability. Biochemistry (2009)

Release Date

2009-05-05

Peptides

Glucosylceramidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glucosylceramidase

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