SMTL ID : 2nsx.7 (8 other biounits)

Structure of acid-beta-glucosidase with pharmacological chaperone provides insight into Gaucher disease

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: I.5, N.19, Y.22 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.5 Water bridges: A:N.19, A:N.19, A:N.19 NAG.8: 1 residues within 4Å: Chain B: N.146 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.146 NAG.9: 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

11 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.12, A:W.357, A:D.358, A:D.358, A:D.358 Salt bridges: A:R.353 SO4.3: 3 residues within 4Å: Chain A: R.44, S.45, Y.487 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.45, A:S.45 Salt bridges: A:R.44 SO4.4: 4 residues within 4Å: Chain A: T.63, G.64, L.65, Q.440 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.63, A:Q.440 SO4.5: 4 residues within 4Å: Chain A: K.79, W.228, R.277, H.306 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.79, A:R.277, A:H.306 SO4.6: 1 residues within 4Å: Chain A: K.473 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.473, A:K.473 Salt bridges: A:K.473 SO4.10: 7 residues within 4Å: Chain A: S.242 Chain B: Y.11, S.12, R.353, S.356, W.357, D.358 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.12, B:S.356, B:W.357, B:D.358, A:S.242 Salt bridges: B:R.353 SO4.11: 2 residues within 4Å: Chain B: R.44, S.45 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.44, B:S.45 Salt bridges: B:R.44 SO4.12: 4 residues within 4Å: Chain B: K.79, W.228, R.277, H.306 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.228 Water bridges: B:K.79 Salt bridges: B:K.79, B:R.277, B:H.306 SO4.13: 4 residues within 4Å: Chain B: G.193, K.194, S.242, G.243 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.194, B:G.243 Water bridges: B:N.188 SO4.14: 2 residues within 4Å: Chain B: K.321, R.329 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.321, B:R.329 SO4.15: 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

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: D.127, F.128, W.179, N.234, E.235, E.340, W.381, F.397 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.179, A:E.235

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

IFM.16: 11 residues within 4Å: Chain B: D.127, F.128, W.179, N.234, E.235, F.246, Y.313, E.340, C.342, W.381, N.396 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.127, B:D.127, B:E.340

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lieberman, R.L. et al., Structure of acid beta-glucosidase with pharmacological chaperone provides insight into Gaucher disease. Nat.Chem.Biol. (2007)

Release Date

2006-12-26

Peptides

Glucosylceramidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glucosylceramidase

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