3GXT

Crystal structure of alpha-galactosidase A at pH 4.5 complexed with 1-deoxygalactonijirimycin

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3gxta2	All beta proteins	Glycosyl hydrolase domain	Glycosyl hydrolase domain	alpha-Amylases, C-terminal beta-sheet domain	Melibiase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3gxta1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	Amylase, catalytic domain	Melibiase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3gxtb2	All beta proteins	Glycosyl hydrolase domain	Glycosyl hydrolase domain	alpha-Amylases, C-terminal beta-sheet domain	Melibiase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3gxtb1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	Amylase, catalytic domain	Melibiase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	(Trans)glycosidases	8040342	3000313	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8040340	3001528	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8040340	3001528	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	(Trans)glycosidases	8040342	3000313	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Melibiase_2_C	e3gxtA1	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: Melibiase_2_C	ECOD (1.6)
A	Glyco_hydro_31_N	e3gxtA2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glyco_hydro_31_N	ECOD (1.6)
B	Melibiase_2_C	e3gxtB1	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: Melibiase_2_C	ECOD (1.6)
B	Glyco_hydro_31_N	e3gxtB2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glyco_hydro_31_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	2.60.40.1180	Mainly Beta	Sandwich	Immunoglobulin-like	Golgi alpha-mannosidase II	CATH (4.3.0)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
B	2.60.40.1180	Mainly Beta	Sandwich	Immunoglobulin-like	Golgi alpha-mannosidase II	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF17450	Alpha galactosidase A C-terminal beta sandwich domain (Melibiase_2_C)	Alpha galactosidase A C-terminal beta sandwich domain	-	Domain
A, B	PF16499	Alpha galactosidase A (Melibiase_2)	Alpha galactosidase A	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Alpha-galactosidase A	protein binding binding signaling receptor binding galactoside binding carbohydrate derivative binding hydrolase activity catalytic activity alpha-galactosidase activity hydrolase activity, acting on glycosyl bonds hydrolase activity, hydrolyzing O-glycosyl compounds galactosidase activity identical protein binding protein homodimerization activity protein dimerization activity	carbohydrate metabolic process oligosaccharide metabolic process primary metabolic process metabolic process negative regulation of monooxygenase activity regulation of catalytic activity negative regulation of oxidoreductase activity biological regulation negative regulation of molecular function negative regulation of catalytic activity regulation of oxidoreductase activity negative regulation of nitric-oxide synthase activity regulation of molecular function regulation of monooxygenase activity carbohydrate metabolic process oligosaccharide metabolic process primary metabolic process metabolic process negative regulation of monooxygenase activity regulation of catalytic activity negative regulation of oxidoreductase activity biological regulation negative regulation of molecular function negative regulation of catalytic activity regulation of oxidoreductase activity negative regulation of nitric-oxide synthase activity regulation of molecular function regulation of monooxygenase activity regulation of nitric-oxide synthase activity regulation of biosynthetic process regulation of nitric oxide biosynthetic process regulation of biological process negative regulation of metabolic process negative regulation of biological process negative regulation of nitric oxide metabolic process reactive nitrogen species metabolic process nitric oxide metabolic process nitric oxide biosynthetic process biosynthetic process negative regulation of nitric oxide biosynthetic process negative regulation of biosynthetic process regulation of nitric oxide metabolic process regulation of metabolic process glycoside catabolic process carbohydrate derivative catabolic process glycosyl compound metabolic process catabolic process glycoside metabolic process carbohydrate derivative metabolic process glycosyl compound catabolic process membrane lipid metabolic process sphingolipid catabolic process glycosphingolipid catabolic process lipid catabolic process glycolipid metabolic process glycosphingolipid metabolic process cellular metabolic process liposaccharide metabolic process sphingolipid metabolic process membrane lipid catabolic process cellular lipid catabolic process cellular catabolic process glycolipid catabolic process cellular lipid metabolic process cellular process lipid metabolic process ceramide catabolic process amide metabolic process glycosylceramide metabolic process ceramide metabolic process glycosylceramide catabolic process	membrane-bounded organelle intracellular anatomical structure lytic vacuole membrane-enclosed lumen vacuolar lumen vacuole cellular anatomical entity intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle organelle lumen organelle cytoplasm membrane-bounded organelle intracellular anatomical structure lytic vacuole membrane-enclosed lumen vacuolar lumen vacuole cellular anatomical entity intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle organelle lumen organelle cytoplasm lysosome extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle intracellular vesicle cytoplasmic vesicle lumen endomembrane system cytoplasmic vesicle vesicle lumen azurophil granule secretory granule lumen azurophil granule lumen secretory granule primary lysosome secretory vesicle Golgi apparatus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B	IPR000111	Glycoside hydrolase family 27/36, conserved site	Conserved Site
A, B	IPR013780	Glycosyl hydrolase, all-beta	Homologous Superfamily
A, B	IPR002241	Glycoside hydrolase, family 27	Family
A, B	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A, B	IPR035373	Alpha galactosidase A, C-terminal beta-sandwich domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P06280	Fabry disease angiokeratoma Pain Disorder subependymal giant cell astrocytoma Charcot-Marie-Tooth disease dilated cardiomyopathy glioblastoma leukodystrophy medulloblastoma pancreatic intraductal papillary-mucinous neoplasm breast fibroadenoma hemangioma hypertrophic cardiomyopathy lysosomal storage disease ovarian cancer Fabry disease angiokeratoma Pain Disorder subependymal giant cell astrocytoma Charcot-Marie-Tooth disease dilated cardiomyopathy glioblastoma leukodystrophy medulloblastoma pancreatic intraductal papillary-mucinous neoplasm breast fibroadenoma hemangioma hypertrophic cardiomyopathy lysosomal storage disease ovarian cancer sphingolipidosis cerebrovascular disorder hydrops fetalis inborn errors of metabolism malignant colon neoplasm

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.