3RIK | pdb_00003rik

The acid beta-glucosidase active site exhibits plasticity in binding 3,4,5,6-tetrahydroxyazepane-based inhibitors: implications for pharmacological chaperone design for gaucher disease

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)
D	d3rikd1	All beta proteins	Glycosyl hydrolase domain	Glycosyl hydrolase domain	Composite domain of glycosyl hydrolase families 5, 30, 39 and 51	Glucosylceramidase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3rikd2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	beta-glycanases	Glucosylceramidase, catalytic domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3rikc1	All beta proteins	Glycosyl hydrolase domain	Glycosyl hydrolase domain	Composite domain of glycosyl hydrolase families 5, 30, 39 and 51	Glucosylceramidase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3rikc2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	beta-glycanases	Glucosylceramidase, catalytic domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3rikb1	All beta proteins	Glycosyl hydrolase domain	Glycosyl hydrolase domain	Composite domain of glycosyl hydrolase families 5, 30, 39 and 51	Glucosylceramidase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3rikb2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	beta-glycanases	Glucosylceramidase, catalytic domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3rika1	All beta proteins	Glycosyl hydrolase domain	Glycosyl hydrolase domain	Composite domain of glycosyl hydrolase families 5, 30, 39 and 51	Glucosylceramidase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3rika2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	beta-glycanases	Glucosylceramidase, catalytic domain	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)
D	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8043253	3001528	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	(Trans)glycosidases	8043254	3000313	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8043253	3001528	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	(Trans)glycosidases	8043254	3000313	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8043253	3001528	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8043253	3001528	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	(Trans)glycosidases	8043254	3000313	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8043253	3001528	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8043253	3001528	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8043253	3001528	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	(Trans)glycosidases	8043254	3000313	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8043253	3001528	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)
D	V-set	e3rikD1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: V-set	ECOD (develop294)
C	V-set	e3rikC1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: V-set	ECOD (develop294)
B	V-set	e3rikB1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: V-set	ECOD (develop294)
A	TED_complement	e3rikA1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: TED_complement	ECOD (develop294)

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	2.60.40.1180	Mainly Beta	Sandwich	Immunoglobulin-like	Golgi alpha-mannosidase II	CATH (4.3.0)
C	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
C	2.60.40.1180	Mainly Beta	Sandwich	Immunoglobulin-like	Golgi alpha-mannosidase II	CATH (4.3.0)
B	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
B	2.60.40.1180	Mainly Beta	Sandwich	Immunoglobulin-like	Golgi alpha-mannosidase II	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, B, C, D	PF17189	Glycosyl hydrolase family 30 beta sandwich domain (Glyco_hydro_30C)	Glycosyl hydrolase family 30 beta sandwich domain		Domain
A, B, C, D	PF02055	Glycosyl hydrolase family 30 TIM-barrel domain (Glyco_hydro_30)	Glycosyl hydrolase family 30 TIM-barrel domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Glucosylceramidase	glycosyltransferase activity transferase activity glucosyltransferase activity hexosyltransferase activity catalytic activity glucosylceramidase activity hydrolase activity, acting on glycosyl bonds glycosylceramidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity protein binding binding signaling receptor binding scavenger receptor binding glycosyltransferase activity transferase activity glucosyltransferase activity hexosyltransferase activity catalytic activity glucosylceramidase activity hydrolase activity, acting on glycosyl bonds glycosylceramidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity protein binding binding signaling receptor binding scavenger receptor binding glucosidase activity steryl-beta-glucosidase activity beta-glucosidase activity galactosylceramidase activity	developmental process stem cell proliferation cell population proliferation cellular developmental process hemopoiesis cell differentiation anatomical structure development hematopoietic stem cell proliferation cell development cellular process carbohydrate derivative biosynthetic process glycolipid metabolic process liposaccharide metabolic process lipid biosynthetic process developmental process stem cell proliferation cell population proliferation cellular developmental process hemopoiesis cell differentiation anatomical structure development hematopoietic stem cell proliferation cell development cellular process carbohydrate derivative biosynthetic process glycolipid metabolic process liposaccharide metabolic process lipid biosynthetic process carbohydrate derivative metabolic process glycolipid biosynthetic process primary metabolic process biosynthetic process metabolic process lipid metabolic process regulation of biological process catabolic process regulation of cellular process macroautophagy autophagy biological regulation regulation of catabolic process regulation of autophagy regulation of macroautophagy process utilizing autophagic mechanism regulation of metabolic process interleukin-6 production multicellular organismal process negative regulation of biological process regulation of interleukin-6 production regulation of cytokine production cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of metabolic process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of interleukin-6 production negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process negative regulation of multicellular organismal process cerebellar cortex morphogenesis hindbrain morphogenesis cerebellar Purkinje cell layer formation multicellular organism development cerebellar Purkinje cell layer development metencephalon development cerebellar Purkinje cell layer morphogenesis cerebellar cortex formation system development cerebellum morphogenesis head development animal organ development brain development nervous system development cerebellar cortex development anatomical structure morphogenesis cerebellum development central nervous system development anatomical structure formation involved in morphogenesis hindbrain development establishment of skin barrier epithelium development skin development skin epidermis development epidermis development tissue development response to ketone response to lipid response to stimulus response to chemical response to oxygen-containing compound response to testosterone regulation of type 2 mitophagy positive regulation of type 2 mitophagy positive regulation of biological process positive regulation of autophagy of mitochondrion positive regulation of metabolic process mitophagy regulation of autophagy of mitochondrion positive regulation of macroautophagy positive regulation of cellular process positive regulation of autophagy positive regulation of mitophagy regulation of mitophagy positive regulation of catabolic process type 2 mitophagy autophagy of mitochondrion positive regulation of proteasomal protein catabolic process positive regulation of protein metabolic process proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of primary metabolic process positive regulation of ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process positive regulation of macromolecule metabolic process protein metabolic process regulation of protein metabolic process proteasomal protein catabolic process protein catabolic process positive regulation of protein catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process regulation of protein catabolic process regulation of cellular component organization negative regulation of cellular component organization protein-containing complex organization regulation of cellular component biogenesis negative regulation of protein-containing complex assembly cellular component organization cellular component biogenesis regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly cellular component organization or biogenesis system process nervous system process neuromuscular process cell activation mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte activation T cell differentiation in thymus T cell activation immune system process T cell differentiation leukocyte differentiation cellular response to stimulus cellular response to nutrient levels response to nutrient levels cellular response to stress response to stress response to starvation cellular response to starvation negative regulation of protein metabolic process response to endogenous stimulus response to glucocorticoid response to corticosteroid response to hormone response to steroid hormone response to dexamethasone regulation of protein catabolic process in the vacuole protein catabolic process in the vacuole lysosomal protein catabolic process regulation of lysosomal protein catabolic process sphingolipid catabolic process ceramide metabolic process carbohydrate derivative catabolic process glycosphingolipid catabolic process lipid catabolic process glycosphingolipid metabolic process sphingolipid metabolic process glucosylceramide metabolic process glycosylceramide catabolic process glycolipid catabolic process ceramide catabolic process glucosylceramide catabolic process glycosylceramide metabolic process positive regulation of cell communication regulation of system process positive regulation of transmission of nerve impulse cell communication neuronal action potential regulation of transmission of nerve impulse positive regulation of nervous system process regulation of biological quality regulation of neuronal action potential regulation of action potential action potential transmission of nerve impulse regulation of nervous system process positive regulation of action potential regulation of cell communication positive regulation of multicellular organismal process positive regulation of neuronal action potential regulation of membrane potential immune system development gland development hematopoietic or lymphoid organ development thymus development response to estrogen multicellular organismal-level homeostasis homeostatic process homeostasis of number of cells polyol metabolic process sphingoid biosynthetic process sphingolipid biosynthetic process small molecule biosynthetic process alcohol metabolic process diol biosynthetic process sphingosine metabolic process sphingoid metabolic process sphingosine biosynthetic process diol metabolic process polyol biosynthetic process alcohol biosynthetic process small molecule metabolic process immune response glycoside catabolic process glycoside metabolic process glycosyl compound catabolic process beta-glucoside catabolic process ceramide biosynthetic process brain morphogenesis animal organ morphogenesis leukocyte migration mononuclear cell migration lymphocyte migration cell migration cell motility regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response negative regulation of response to stimulus response to external stimulus regulation of inflammatory response regulation of response to stimulus negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response regulation of signaling negative regulation of signaling signaling termination of signal transduction regulation of signal transduction negative regulation of signal transduction negative regulation of cell communication signal transduction secondary alcohol metabolic process sterol metabolic process steroid metabolic process cholesterol metabolic process neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death regulation of neuron apoptotic process lysosome organization organelle organization vacuole organization lytic vacuole organization myeloid leukocyte differentiation macrophage differentiation neurogenesis gliogenesis glial cell differentiation myeloid cell differentiation microglia differentiation anatomical structure maturation cell maturation developmental maturation response to peptide cellular response to tumor necrosis factor response to cytokine cellular response to cytokine stimulus response to tumor necrosis factor response to pH response to abiotic stimulus negative regulation of intracellular signal transduction intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette regulation of MAPK cascade MAPK cascade negative regulation of MAPK cascade determination of adult lifespan response to thyroid hormone lipid storage nutrient storage generation of neurons central nervous system neuron differentiation neuron differentiation pyramidal neuron differentiation microglial cell proliferation leukocyte proliferation macrophage proliferation glial cell proliferation behavior motor behavior antigen processing and presentation TOR signaling regulation of TOR signaling cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain generation of precursor metabolites and energy autophagosome organization	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle vacuolar membrane intracellular anatomical structure membrane lytic vacuole extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle vacuolar membrane intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle lysosomal membrane cytoplasm organelle membrane lysosome Golgi apparatus subcompartment Golgi apparatus organelle subcompartment endomembrane system trans-Golgi network membrane-enclosed lumen vacuolar lumen lysosomal lumen intracellular organelle lumen organelle lumen endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR033452	Glycosyl hydrolase family 30, beta sandwich domain	Domain
A, B, C, D	IPR001139	Glycoside hydrolase family 30	Family
A, B, C, D	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A, B, C, D	IPR033453	Glycosyl hydrolase family 30, TIM-barrel domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P04062	Gaucher disease Parkinson disease Gaucher disease-ophthalmoplegia-cardiovascular calcification syndrome Lewy body dementia Gaucher disease perinatal lethal late-onset Parkinson disease Gaucher disease type II pulmonary hypertension Gaucher disease type III Gaucher disease type I Gaucher Disease, Type 2 (disorder) arthrogryposis mucolipidosis type IV brain aneurysm Crohn disease Gaucher disease Parkinson disease Gaucher disease-ophthalmoplegia-cardiovascular calcification syndrome Lewy body dementia Gaucher disease perinatal lethal late-onset Parkinson disease Gaucher disease type II pulmonary hypertension Gaucher disease type III Gaucher disease type I Gaucher Disease, Type 2 (disorder) arthrogryposis mucolipidosis type IV brain aneurysm Crohn disease psoriasis Riley-Day syndrome hematopoietic and lymphoid system neoplasm inborn errors of metabolism neurodegenerative disease autosomal recessive juvenile Parkinson disease 2 parkinsonian disorder cholestasis dental caries hydrops fetalis intellectual disability lysosomal storage disease Niemann-Pick disease type B diabetes mellitus gastric adenocarcinoma sphingolipidosis

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.