3WF0 | pdb_00003wf0

Crystal structure of human beta-galactosidase in complex with 6S-NBI-DGJ

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)
D	KOG0496	e3wf0D2	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	e3wf0D3	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	e3wf0D1	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	e3wf0C2	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	e3wf0C3	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	e3wf0C1	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	e3wf0B2	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	e3wf0B3	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	e3wf0B1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glyco_hydro_42	ECOD (1.6)
A	KOG0496	e3wf0A2	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	e3wf0A3	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	e3wf0A1	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)
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)
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)
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)
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)

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 cellular process carbohydrate derivative catabolic process glycoprotein catabolic process catabolic process keratan sulfate proteoglycan metabolic process carbohydrate derivative metabolic process protein catabolic process keratan sulfate proteoglycan catabolic process glycoprotein metabolic process macromolecule catabolic process protein metabolic process carbohydrate metabolic process primary metabolic process metabolic process cellular process carbohydrate derivative catabolic process glycoprotein catabolic process catabolic process keratan sulfate proteoglycan metabolic process carbohydrate derivative metabolic process protein catabolic process keratan sulfate proteoglycan catabolic process glycoprotein metabolic process macromolecule catabolic process protein metabolic process macromolecule metabolic process proteoglycan metabolic process proteoglycan catabolic process response to Thyroglobulin triiodothyronine response to stimulus response to chemical membrane lipid metabolic process sphingolipid catabolic process ceramide metabolic process ganglioside catabolic process glycosphingolipid catabolic process lipid catabolic process glycolipid metabolic process glycosphingolipid metabolic process liposaccharide metabolic process sphingolipid metabolic process membrane lipid catabolic process glycolipid catabolic process ceramide catabolic process amide metabolic process ganglioside metabolic process lipid metabolic process heparan sulfate proteoglycan metabolic process heparan sulfate proteoglycan catabolic 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 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	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle organelle lumen organelle cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole 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 inborn errors of metabolism 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 inborn errors of metabolism allergic rhinitis lysosomal storage disease ovarian cancer diabetes mellitus Schwartz-Jampel syndrome endogenous depression spondyloepiphyseal dysplasia tarda, X-linked glioblastoma intellectual disability asthma malignant glioma atypical teratoid rhabdoid tumor celiac disease pancreatic ductal adenocarcinoma sphingolipidosis tuberculosis hypertrophic cardiomyopathy leukodystrophy astrocytic tumor 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.