3gxi Summary


Crystal structure of acid-beta-glucosidase at pH 5.5

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

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