3gxf Summary

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Crystal structure of acid-beta-glucosidase with isofagomine at neutral pH

The structure was published by Lieberman, R.L., D'aquino, J.A., Ringe, D., and Petsko, G.A., in 2009 in a paper entitled "Effects of pH and iminosugar pharmacological chaperones on lysosomal glycosidase structure and stability." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.4 Å and deposited in 2009.

The experimental data on which the structure is based was also deposited.

This PDB entry contains multiple copies of the structure of Glucosylceramidase.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule has more than one probable quaternary state observed. For more details see the quaternary structure page.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A Glucosylceramidase P04062 (40-536) (GLCM_HUMAN)search Homo sapienssearch 96% 497 100%
B Glucosylceramidase P04062 (40-536) (GLCM_HUMAN)search Homo sapienssearch 96% 497 100%
C Glucosylceramidase P04062 (40-536) (GLCM_HUMAN)search Homo sapienssearch 96% 497 100%
D Glucosylceramidase P04062 (40-536) (GLCM_HUMAN)search Homo sapienssearch 96% 497 100%


This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
P04062 (40 - 536) Glucosylceramidase Homo sapiens

Chain Structural classification (CATH) Sequence family (Pfam)
A, B, C, D (P04062) Glycosidasessearch, Golgi alpha-mannosidase IIsearch PF02055: O-Glycosyl hydrolase family 30search

Chain ID Molecular function (GO) Cellular component (GO) Biological process (GO)
A, B, C, D (P04062) glucosylceramidase activitysearch hydrolase activitysearch receptor bindingsearch hydrolase activity, acting on glycosyl bondssearch protein bindingsearch lysosomal lumensearch lysosomesearch lysosomal membranesearch extracellular vesicular exosomesearch membranesearch cellular response to tumor necrosis factorsearch negative regulation of inflammatory responsesearch skin morphogenesissearch sphingolipid metabolic processsearch cell deathsearch negative regulation of MAP kinase activitysearch sphingosine biosynthetic processsearch regulation of water loss via skinsearch response to estrogensearch response to thyroid hormonesearch negative regulation of interleukin-6 productionsearch lipid metabolic processsearch metabolic processsearch carbohydrate metabolic processsearch glycosphingolipid metabolic processsearch small molecule metabolic processsearch positive regulation of protein dephosphorylationsearch response to testosteronesearch termination of signal transductionsearch ceramide biosynthetic processsearch response to pHsearch response to glucocorticoidsearch glucosylceramide catabolic processsearch

Chain InterPro annotation
A, B, C, D Glycoside hydrolase, family 30search Glycosyl hydrolase, family 13, all-betasearch Glycoside hydrolase, catalytic domainsearch Glycoside hydrolase superfamilysearch