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

Crystal Structure of N370S Glucocerebrosidase mutant at pH 7.4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

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.1: 2 residues within 4Å: Chain A: N.19, T.21 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: N.19, T.21 No protein-ligand interaction detected (PLIP)

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

SO4.2: 4 residues within 4Å: Chain A: K.79, W.228, R.277, H.306 Ligand excluded by PLIP SO4.3: 7 residues within 4Å: Chain A: Y.11, S.12, R.353, S.356, W.357, D.358 Chain D: S.242 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: R.44, S.465, Y.487 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain B: K.79, W.228, R.277, H.306 Ligand excluded by PLIP SO4.9: 7 residues within 4Å: Chain B: Y.11, S.12, R.353, S.356, W.357, D.358 Chain C: S.242 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain B: R.44, S.465, Y.487 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain C: E.254, R.257, V.294 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain C: Q.169, R.170, P.428 Ligand excluded by PLIP SO4.16: 6 residues within 4Å: Chain C: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain C: K.79, W.228, R.277, H.306 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain C: R.329, L.330 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain D: E.254, R.257, V.294 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain D: Q.169, R.170, P.428 Ligand excluded by PLIP SO4.24: 6 residues within 4Å: Chain D: Y.11, S.12, R.353, S.356, W.357, D.358 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain D: K.79, W.228, R.277, H.306 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain D: R.329, L.330 Ligand excluded by PLIP

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

NAG.5: 3 residues within 4Å: Chain A: T.138, N.146 Chain C: P.98 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.138 NAG.11: 3 residues within 4Å: Chain B: T.138, N.146 Chain D: P.98 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.138 Hydrogen bonds: B:T.138 NAG.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NAG.28: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 9 residues within 4Å: Chain A: D.127, F.128, W.179, N.234, E.235, F.246, E.340, W.381, N.396 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.179, A:N.234, A:N.234, A:W.381, A:N.396 GOL.12: 9 residues within 4Å: Chain B: D.127, F.128, W.179, N.234, E.235, F.246, E.340, W.381, N.396 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.179, B:N.234, B:N.234, B:W.381, B:N.396 GOL.19: 7 residues within 4Å: Chain C: R.2, D.24, S.25, F.26, R.48, M.49, Y.418 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.24, C:D.24, C:D.24 GOL.27: 7 residues within 4Å: Chain D: R.2, D.24, S.25, F.26, R.48, M.49, Y.418 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.24, D:D.24

2 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)

NDG.13: 4 residues within 4Å: Chain C: I.5, N.19, T.21, Y.22 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.19, C:T.21 NDG.21: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wei, R.R. et al., Crystal Structure of Glucocerebrosidase Containing the N370S mutation: Implication on Chaperon Therapy. To be Published

Release Date

2010-10-27

Peptides

Glucocerebrosidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
A

D
A

Glucocerebrosidase

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