3THD

Crystal structure of human beta-galactosidase in complex with 1-deoxygalactonojirimycin

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	KOG0496	e3thdA2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: KOG0496	ECOD (1.6)
A	BetaGal_dom4_5_2	e3thdA1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: BetaGal_dom4_5_2	ECOD (1.6)
A	Glyco_hydro_42	e3thdA3	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glyco_hydro_42	ECOD (1.6)
B	KOG0496	e3thdB3	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: KOG0496	ECOD (1.6)
B	BetaGal_dom4_5_2	e3thdB1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: BetaGal_dom4_5_2	ECOD (1.6)
B	Glyco_hydro_42	e3thdB2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glyco_hydro_42	ECOD (1.6)
C	KOG0496	e3thdC8	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: KOG0496	ECOD (1.6)
C	BetaGal_dom4_5_2	e3thdC9	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: BetaGal_dom4_5_2	ECOD (1.6)
C	Glyco_hydro_42	e3thdC7	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glyco_hydro_42	ECOD (1.6)
D	KOG0496	e3thdD2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: KOG0496	ECOD (1.6)
D	BetaGal_dom4_5_2	e3thdD3	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: BetaGal_dom4_5_2	ECOD (1.6)
D	Glyco_hydro_42	e3thdD1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glyco_hydro_42	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
A	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
B	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
B	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
C	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
C	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
D	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
D	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF21317	Beta-galactosidase, first all-beta domain (BetaGal_ABD_1)	Beta-galactosidase, first all-beta domain	Beta-galactosidases belong to glycosyl hydrolase 35 family (GH35) which catalyse the cleaveage of beta-linked terminal galactosyl residues from gangliosides, glycoproteins, and glycosaminoglycans. These proteins consist of a catalytic TIM-barrel and ...	Beta-galactosidases belong to glycosyl hydrolase 35 family (GH35) which catalyse the cleaveage of beta-linked terminal galactosyl residues from gangliosides, glycoproteins, and glycosaminoglycans. These proteins consist of a catalytic TIM-barrel and two all-beta domains (ABD1 and ABD2) [1-5]. This entry represents the first all-beta domain ABD1. ABD2 is represented in Pfam:PF13364.	Domain
A, B, C, D	PF01301	Glycosyl hydrolases family 35 (Glyco_hydro_35)	Glycosyl hydrolases family 35	-	Domain
A, B, C, D	PF21467	Beta-galactosidase, galactose-binding domain (BetaGal_gal-bd)	Beta-galactosidase, galactose-binding domain	Beta-galactosidase belongs to Glycoside hydrolase family 35 [1-5]. This entry represents the galactose-binding domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Beta-galactosidase	hydrolase activity, acting on glycosyl bonds beta-galactosidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity galactosidase activity galactoside binding binding carbohydrate derivative binding identical protein binding protein binding protein homodimerization activity protein dimerization activity	carbohydrate metabolic process primary metabolic process metabolic process response to Thyroglobulin triiodothyronine response to stimulus response to chemical mucopolysaccharide metabolic process carbohydrate derivative catabolic process keratan sulfate catabolic process catabolic process cellular metabolic process glycosaminoglycan metabolic process carbohydrate derivative metabolic process aminoglycan catabolic process carbohydrate metabolic process primary metabolic process metabolic process response to Thyroglobulin triiodothyronine response to stimulus response to chemical mucopolysaccharide metabolic process carbohydrate derivative catabolic process keratan sulfate catabolic process catabolic process cellular metabolic process glycosaminoglycan metabolic process carbohydrate derivative metabolic process aminoglycan catabolic process macromolecule catabolic process cellular catabolic process sulfur compound catabolic process glycosaminoglycan catabolic process aminoglycan metabolic process keratan sulfate metabolic process sulfur compound metabolic process cellular process macromolecule metabolic process membrane lipid metabolic process sphingolipid catabolic process glycosphingolipid catabolic process lipid catabolic process glycolipid metabolic process glycosphingolipid metabolic process liposaccharide metabolic process sphingolipid metabolic process membrane lipid catabolic process cellular lipid catabolic process glycolipid catabolic process cellular lipid metabolic process lipid metabolic process glycoprotein catabolic process protein catabolic process glycoprotein metabolic process heparan sulfate proteoglycan catabolic process protein metabolic process proteoglycan catabolic process proteoglycan metabolic process response to ketone response to lipid response to endogenous stimulus response to alcohol response to glucocorticoid response to oxygen-containing compound response to corticosteroid response to hormone response to steroid hormone response to cortisone response to organic cyclic compound monosaccharide metabolic process hexose catabolic process carbohydrate catabolic process galactose catabolic process hexose metabolic process galactose metabolic process small molecule metabolic process monosaccharide catabolic process small molecule 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 ficolin-1-rich granule ficolin-1-rich granule lumen Golgi apparatus perinuclear region of cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR048913	Beta-galactosidase, galactose-binding domain	Domain
A, B, C, D	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR019801	Glycoside hydrolase, family 35, conserved site	Conserved Site
A, B, C, D	IPR001944	Glycoside hydrolase, family 35	Family
A, B, C, D	IPR031330	Glycoside hydrolase 35, catalytic domain	Domain
A, B, C, D	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A, B, C, D	IPR026283	Beta-galactosidase 1-like	Family
A, B, C, D	IPR048912	Beta-galactosidase 1-like , first all-beta domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P16278	GM1 gangliosidosis mucopolysaccharidosis mucopolysaccharidosis type 4 mucopolysaccharidosis type 4B osteochondrodysplasia GM1 gangliosidosis type 1 atopic eczema Bone Diseases, Developmental gangliosidosis GM1 gangliosidosis type 2 multiple epiphyseal dysplasia GM1 gangliosidosis type 3 contact dermatitis hydrops fetalis allergic rhinitis GM1 gangliosidosis mucopolysaccharidosis mucopolysaccharidosis type 4 mucopolysaccharidosis type 4B osteochondrodysplasia GM1 gangliosidosis type 1 atopic eczema Bone Diseases, Developmental gangliosidosis GM1 gangliosidosis type 2 multiple epiphyseal dysplasia GM1 gangliosidosis type 3 contact dermatitis hydrops fetalis allergic rhinitis inborn errors of metabolism lysosomal storage disease diabetes mellitus ovarian cancer endogenous depression Schwartz-Jampel syndrome spondyloepiphyseal dysplasia tarda, X-linked glioblastoma asthma intellectual disability atypical teratoid rhabdoid tumor malignant glioma celiac disease pancreatic ductal adenocarcinoma sphingolipidosis tuberculosis hypertrophic cardiomyopathy astrocytic tumor leukodystrophy Melnick-Needles syndrome dermatitis, atopic plasma cell myeloma spondyloepiphyseal dysplasia

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.