SMTL ID : 3gxm.3 (3 other biounits)

Crystal structure of acid-beta-glucosidase at pH 4.5, phosphate crystallization condition

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: I.5, N.19, T.21, Y.22 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.19, A:N.19, A:N.19, A:T.21 NAG.10: 4 residues within 4Å: Chain B: I.5, N.19, T.21, Y.22 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.21 Water bridges: B:N.19, B:N.19, B:N.19, B:N.19

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

SO4.2: 6 residues within 4Å: Chain A: Y.11, S.12, R.353, S.356, W.357, D.358 11 PLIP interactions: 1 interactions with chain B, 10 interactions with chain A Water bridges: B:S.242, A:S.12, A:R.353, A:R.353, A:R.353, A:D.358 Hydrogen bonds: A:S.12, A:S.12, A:W.357, A:D.358 Salt bridges: A:R.353 SO4.3: 3 residues within 4Å: Chain A: T.63, G.64, Q.440 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.63, A:Q.440 SO4.4: 4 residues within 4Å: Chain A: K.79, W.228, R.277, H.306 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.228 Salt bridges: A:K.79, A:R.277, A:H.306 SO4.5: 5 residues within 4Å: Chain A: Y.11, W.348, E.349, Q.350, R.353 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.11, A:Q.350 Salt bridges: A:R.353 SO4.6: 3 residues within 4Å: Chain A: R.44, S.465, Y.487 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.487 Water bridges: A:S.465, A:S.465 Salt bridges: A:R.44 SO4.7: 3 residues within 4Å: Chain A: E.254, R.257 Chain B: K.441 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:K.441, A:R.257 Water bridges: A:E.254, A:R.257 SO4.8: 2 residues within 4Å: Chain A: H.290, K.293 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.290, A:K.293 SO4.9: 2 residues within 4Å: Chain A: R.44, S.45 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.44, A:S.45, A:S.45, A:S.465, A:G.486 Salt bridges: A:R.44 SO4.11: 7 residues within 4Å: Chain A: S.242 Chain B: Y.11, S.12, R.353, S.356, W.357, D.358 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.12, B:S.12, B:S.12, B:W.357, B:D.358, A:S.242 Water bridges: B:R.353, B:S.356 Salt bridges: B:R.353 SO4.12: 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 SO4.13: 4 residues within 4Å: Chain B: K.79, W.228, R.277, H.306 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:W.228 Water bridges: B:R.277, B:R.277, B:E.429 Salt bridges: B:K.79, B:R.277, B:H.306 SO4.14: 5 residues within 4Å: Chain B: Q.226, T.272, H.273, N.275, V.276 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.226 Water bridges: B:F.227, B:T.272, B:H.273, B:N.275, B:N.275, B:N.275 Salt bridges: B:H.273 SO4.15: 2 residues within 4Å: Chain B: R.44, S.45 3 PLIP interactions: 3 interactions with chain B Water bridges: B:S.45, B:S.45 Salt bridges: B:R.44 SO4.16: 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 SO4.17: 3 residues within 4Å: Chain B: R.277, V.305, H.306 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.305 Water bridges: B:R.277, B:H.306 Salt bridges: B:R.277, B:H.306

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glucosylceramidase

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