5NN5

Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with 1-deoxynojirimycin

External Resource: Annotation

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
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Galactose mutarotase-like	8093233	3000035	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Trefoil	8093235	3000849	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8093239	3001528	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	YicI C-terminal domain-like	8093241	3000267	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	(Trans)glycosidases	8093237	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	Glyco_hydro_31_C	e5nn5A4	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: Glyco_hydro_31_C	ECOD (1.6)
A	Gal_mutarotas_2,Trefoil	e5nn5A2	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich (From Topology)	T: supersandwich	F: Gal_mutarotas_2,Trefoil	ECOD (1.6)
A	DUF5110_1	e5nn5A1	A: beta sandwiches	X: Putative glucosidase YicI, C-terminal domain (From Topology)	H: Putative glucosidase YicI, C-terminal domain (From Topology)	T: Putative glucosidase YicI, C-terminal domain	F: DUF5110_1	ECOD (1.6)
A	Glyco_hydro_31_N	e5nn5A3	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	4.10.110.10	Few Secondary Structures	Irregular	Spasmolytic Protein	domain 1	CATH (4.3.0)
A	2.60.40.1760	Mainly Beta	Sandwich	Immunoglobulin-like	glycosyl hydrolase (family 31)	CATH (4.3.0)
A	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
A	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	PF21365	Glycosyl hydrolase family 31 C-terminal domain (Glyco_hydro_31_3rd)	Glycosyl hydrolase family 31 C-terminal domain	Glycosyl hydrolases are key enzymes of carbohydrate metabolism. Family 31 comprises of enzymes that are, or similar to, alpha- galactosidases. This entry represents the 3rd beta sandwich domain.	Domain
A	PF13802	Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain (Gal_mutarotas_2)	Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain	This entry represents the first of three common domains found in Glycosyl hydrolase 31 family proteins. It has a galactose mutarotase superfamily fold.	Domain
A	PF01055	Glycosyl hydrolases family 31 TIM-barrel domain (Glyco_hydro_31_2nd)	Glycosyl hydrolases family 31 TIM-barrel domain	Glycosyl hydrolases are key enzymes of carbohydrate metabolism. Family 31 comprises of enzymes that are, or similar to, alpha- galactosidases. This entry corresponds to the second domain of family 31 enzymes and adopts a TIM-barrel fold.	Domain
A	PF00088	Trefoil (P-type) domain (Trefoil)	Trefoil (P-type) domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Lysosomal alpha-glucosidase	alpha-glucosidase activity hydrolase activity, acting on glycosyl bonds glucosidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity alpha-1,4-glucosidase activity binding carbohydrate binding	carbohydrate metabolic process catabolic process glucan catabolic process energy derivation by oxidation of organic compounds macroautophagy glycogen metabolic process carbohydrate catabolic process autophagy primary metabolic process generation of precursor metabolites and energy macromolecule catabolic process polysaccharide metabolic process glucan metabolic process glycogen catabolic process glycophagy carbohydrate metabolic process catabolic process glucan catabolic process energy derivation by oxidation of organic compounds macroautophagy glycogen metabolic process carbohydrate catabolic process autophagy primary metabolic process generation of precursor metabolites and energy macromolecule catabolic process polysaccharide metabolic process glucan metabolic process glycogen catabolic process glycophagy polysaccharide catabolic process metabolic process cellular process energy reserve metabolic process macromolecule metabolic process process utilizing autophagic mechanism behavior multicellular organismal process locomotory behavior sucrose metabolic process oligosaccharide metabolic process disaccharide metabolic process heart process system process regulation of biological process regulation of heart contraction regulation of system process biological regulation circulatory system process regulation of blood circulation regulation of multicellular organismal process regulation of biological quality heart contraction regulation of the force of heart contraction blood circulation developmental process anatomical structure development tissue development nervous system process neuromuscular process skeletal muscle contraction muscle contraction respiratory gaseous exchange by respiratory system muscle system process striated muscle contraction multicellular organismal movement musculoskeletal movement diaphragm contraction respiratory system process involuntary skeletal muscle contraction neuromuscular process controlling balance multicellular organism development artery development aorta development vasculature development blood vessel development system development circulatory system development cellular component organization lysosome organization organelle organization vacuole organization lytic vacuole organization cellular component organization or biogenesis monosaccharide metabolic process hexose metabolic process small molecule metabolic process glucose metabolic process heart development heart morphogenesis animal organ development anatomical structure morphogenesis animal organ morphogenesis cardiac muscle contraction neuromuscular process controlling posture maltose metabolic process localization cellular localization vacuolar sequestering maintenance of location in cell maintenance of location cellular homeostasis homeostatic process muscle cell cellular homeostasis	membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane lytic vacuole membrane-enclosed lumen vacuolar lumen vacuole lysosomal lumen intracellular organelle lumen organelle lumen lysosome extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle vacuolar membrane azurophil granule lytic vacuole membrane lysosomal membrane primary lysosome azurophil granule membrane cell periphery plasma membrane autolysosome secondary lysosome autolysosome lumen ficolin-1-rich granule membrane ficolin-1-rich granule

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR048395	Glycosyl hydrolase family 31, C-terminal domain	Domain
A	IPR013780	Glycosyl hydrolase, all-beta	Homologous Superfamily
A	IPR025887	Glycoside hydrolase family 31, N-terminal domain	Domain
A	IPR044913	P-type trefoil domain superfamily	Homologous Superfamily
A	IPR030459	Glycosyl hydrolases family 31, conserved site	Conserved Site
A	IPR000322	Glycoside hydrolase family 31, TIM barrel domain	Domain
A	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A	IPR000519	P-type trefoil domain	Domain
A	IPR030458	Glycosyl hydrolases family 31, active site	Active Site
A	IPR017957	P-type trefoil, conserved site	Conserved Site
A	IPR011013	Galactose mutarotase-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P10253	glycogen storage disease II membranous glomerulonephritis hypertrophic cardiomyopathy glycogen storage disease Ventricular Dysfunction intellectual disability limb-girdle muscular dystrophy psoriasis type 2 diabetes mellitus glycogen storage disease due to acid maltase deficiency, infantile onset idiopathic membranous glomerulonephritis malignant glioma ovarian cancer rhabdomyolysis arthrogryposis glycogen storage disease II membranous glomerulonephritis hypertrophic cardiomyopathy glycogen storage disease Ventricular Dysfunction intellectual disability limb-girdle muscular dystrophy psoriasis type 2 diabetes mellitus glycogen storage disease due to acid maltase deficiency, infantile onset idiopathic membranous glomerulonephritis malignant glioma ovarian cancer rhabdomyolysis arthrogryposis Charcot-Marie-Tooth disease glioblastoma glycogen storage disease due to acid maltase deficiency, late-onset inborn errors of metabolism malignant mesothelioma pilocytic astrocytoma tuberculosis breast carcinoma Gaucher disease

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	CSO	Parent Component: CYS RESID: AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210

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.