3gxd Summary

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Crystal structure of Apo acid-beta-glucosidase pH 4.5

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 2.5 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 most likely forms homotetramers.

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

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