SMTL ID : 2wcg.1 (1 other biounit)

X-ray structure of acid-beta-glucosidase with N-octyl(cyclic guanidine)-nojirimycin in the active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 4 residues within 4Å: Chain A: N.21, T.23, Y.24 Ligands: FUC.2 No protein-ligand interaction detected (PLIP)

1 x FUC: alpha-L-fucopyranose(Non-functional Binders)

FUC.2: 2 residues within 4Å: Ligands: NAG-NAG-BMA.1, NAG-NAG-BMA.1 No protein-ligand interaction detected (PLIP)

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

SO4.3: 6 residues within 4Å: Chain A: Y.13, S.14, R.355, S.358, W.359, D.360 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.14, A:S.14, A:S.358, A:W.359, A:D.360 Water bridges: A:R.355, A:S.358 Salt bridges: A:R.355 SO4.4: 4 residues within 4Å: Chain A: K.81, W.230, R.279, H.308 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.431 Salt bridges: A:K.81, A:R.279, A:H.308 SO4.5: 4 residues within 4Å: Chain A: G.195, K.196, S.244, G.245 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.196, A:G.245 Water bridges: A:N.190, A:K.196 SO4.6: 2 residues within 4Å: Chain A: R.46, S.47 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.46, A:S.47 Salt bridges: A:R.46 SO4.7: 2 residues within 4Å: Chain A: E.256, R.259 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.256, A:R.259 Salt bridges: A:R.259 SO4.8: 3 residues within 4Å: Chain A: R.46, S.467, Y.489 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.489 Salt bridges: A:R.46

1 x MT5: N-[(3E,5R,6R,7S,8R,8AR)-5,6,7,8-TETRAHYDROXYHEXAHYDROIMIDAZO[1,5-A]PYRIDIN-3(2H)-YLIDENE]OCTAN-1-AMINIUM(Non-covalent)

MT5.9: 13 residues within 4Å: Chain A: D.129, F.130, W.181, N.236, E.237, F.248, Y.315, E.342, C.344, S.347, W.383, N.398, V.400 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:W.181, A:N.236, A:E.237, A:N.398 Water bridges: A:E.237, A:N.398, A:N.398 Salt bridges: A:E.237 pi-Stacking: A:Y.315 pi-Cation interactions: A:Y.315

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 1 residues within 4Å: Chain A: R.355 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brumshtein, B. et al., 6-Amino-6-Deoxy-5,6-Di-N-(N'-Octyliminomethylidene)Nojirimycin: Synthesis, Biological Evaluation, and Crystal Structure in Complex with Acid Beta-Glucosidase. Chembiochem (2009)

Release Date

2009-11-24

Peptides

GLUCOSYLCERAMIDASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GLUCOSYLCERAMIDASE

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