SMTL ID : 3ke0.3 (2 other biounits)

Crystal structure of N370S Glucocerebrosidase at acidic pH.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

2 x NDG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose(Post Translational Modification)

NDG-NAG.1: 4 residues within 4Å: Chain A: I.5, N.19, T.21, Y.22 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.5, A:T.21 Hydrogen bonds: A:T.21 NDG-NAG.12: 4 residues within 4Å: Chain B: I.5, N.19, T.21, Y.22 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.5, B:T.21 Hydrogen bonds: B:T.21

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

SO4.2: 2 residues within 4Å: Chain A: R.44, Y.487 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain A: E.254, R.257 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: Q.169, R.170, P.428 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain A: R.44, S.45 Ligand excluded by PLIP SO4.6: 6 residues within 4Å: Chain A: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: T.63, G.64, Q.440 Chain B: K.473 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: K.79, W.228, R.277, H.306 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: R.329, L.330 Chain C: K.321, R.329 Ligand excluded by PLIP SO4.13: 2 residues within 4Å: Chain B: R.44, Y.487 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain B: E.254, R.257 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain B: Q.169, R.170, P.428 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain B: R.44, S.45 Ligand excluded by PLIP SO4.17: 6 residues within 4Å: Chain B: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain A: K.473 Chain B: T.63, G.64, Q.440 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain B: K.79, W.228, R.277, H.306 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain B: R.329, L.330 Chain D: K.321, R.329 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain C: G.193, K.194, S.242, G.243 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain C: K.79, W.228, R.277, H.306 Ligand excluded by PLIP SO4.26: 7 residues within 4Å: Chain B: S.242 Chain C: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain C: R.44, S.45 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain C: R.44, S.465, Y.487 Ligand excluded by PLIP SO4.32: 4 residues within 4Å: Chain D: G.193, K.194, S.242, G.243 Ligand excluded by PLIP SO4.33: 4 residues within 4Å: Chain D: K.79, W.228, R.277, H.306 Ligand excluded by PLIP SO4.34: 7 residues within 4Å: Chain A: S.242 Chain D: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP SO4.35: 2 residues within 4Å: Chain D: R.44, S.45 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain D: R.44, S.465, Y.487 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 7 residues within 4Å: Chain A: R.2, D.24, S.25, F.26, R.48, M.49, Y.418 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.24, A:D.24 GOL.11: 2 residues within 4Å: Chain A: V.394, R.395 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.394 GOL.21: 7 residues within 4Å: Chain B: R.2, D.24, S.25, F.26, R.48, M.49, Y.418 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.24 GOL.22: 2 residues within 4Å: Chain B: V.394, R.395 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.394 GOL.30: 10 residues within 4Å: Chain C: D.127, F.128, W.179, N.234, E.235, F.246, Y.313, E.340, W.381, N.396 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:W.179, C:N.234, C:E.235, C:W.381, C:N.396 GOL.38: 10 residues within 4Å: Chain D: D.127, F.128, W.179, N.234, E.235, F.246, Y.313, E.340, W.381, N.396 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:W.179, D:N.234, D:E.235, D:W.381, D:N.396

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.23: 4 residues within 4Å: Chain C: I.5, N.19, T.21, Y.22 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 4 residues within 4Å: Chain D: I.5, N.19, T.21, Y.22 No protein-ligand interaction detected (PLIP)

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

NAG.29: 1 residues within 4Å: Chain C: N.146 No protein-ligand interaction detected (PLIP) NAG.37: 1 residues within 4Å: Chain D: N.146 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wei, R.R. et al., Crystal Structure of Glucocerebrosidase Containing the N370S Mutation, Implications for Chaperon Therapy. To be Published

Release Date

2010-10-27

Peptides

Glucosylceramidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
B

D
B

Glucosylceramidase

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