3igu Summary

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Crystal structure of human alpha-N-acetylgalactosaminidase, covalent intermediate

The structure was published by Clark, N.E. and Garman, S.C., in 2009 in a paper entitled "The 1.9 a structure of human alpha-N-acetylgalactosaminidase: The molecular basis of Schindler and Kanzaki diseases" (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.15 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 Alpha-N-acetylgalactosaminidase.

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 homodimers.

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 Alpha-N-acetylgalactosaminidase P17050 (18-411) (NAGAB_HUMAN)search Homo sapienssearch 100% 400 96%
B Alpha-N-acetylgalactosaminidase P17050 (18-411) (NAGAB_HUMAN)search Homo sapienssearch 100% 400 96%


This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
P17050 (18 - 411) Alpha-N-acetylgalactosaminidase Homo sapiens

Chain Structural classification (CATH) Sequence family (Pfam)
A, B (P17050) Aldolase class Isearch, Golgi alpha-mannosidase IIsearch PF02065: Melibiasesearch

Chain ID Cellular component (GO) Molecular function (GO) Biological process (GO)
A, B (P17050) extracellular vesicular exosomesearch lysosomesearch cytoplasmsearch alpha-galactosidase activitysearch hydrolase activity, acting on glycosyl bondssearch hydrolase activity, hydrolyzing O-glycosyl compoundssearch catalytic activitysearch hydrolase activitysearch alpha-N-acetylgalactosaminidase activitysearch protein homodimerization activitysearch carbohydrate metabolic processsearch glycoside catabolic processsearch oligosaccharide metabolic processsearch glycosylceramide catabolic processsearch metabolic processsearch glycolipid catabolic processsearch carbohydrate catabolic processsearch

Chain InterPro annotation
A, B Glycoside hydrolase, clan GH-Dsearch Glycoside hydrolase, family 27search Glycosyl hydrolase, family 13, all-betasearch Aldolase-type TIM barrelsearch Glycoside hydrolase superfamilysearch