4BZY | pdb_00004bzy

Crystal structure of human glycogen branching enzyme (GBE1)

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)
C	Vinculin	e4bzyC1	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Vinculin	ECOD (develop294)
B	CBM_48	e4bzyB3	A: alpha bundles	X: HAMP domain	H: HAMP domain	T: HAMP domain	F: CBM_48	ECOD (develop294)
B	Ig_2	e4bzyB8	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Ig_2	ECOD (develop294)
A	Ig_2	e4bzyA10	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Ig_2	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	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	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	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	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	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	PF02922	Carbohydrate-binding module 48 (Isoamylase N-terminal domain) (CBM_48)	Carbohydrate-binding module 48 (Isoamylase N-terminal domain)	This domain is found in a range of enzymes that act on branched substrates - isoamylase, pullulanase and branching enzyme. This family also contains the beta subunit of 5' AMP activated kinase.	Domain
A, B, C	PF00128	Alpha amylase, catalytic domain (Alpha-amylase)	Alpha amylase, catalytic domain	Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, a ...	Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain.	Domain
A, B, C	PF02806	Alpha amylase, C-terminal all-beta domain (Alpha-amylase_C)	Alpha amylase, C-terminal all-beta domain	Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, a ...	Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	1,4-ALPHA-GLUCAN-BRANCHING ENZYME	binding carbohydrate binding 1,4-alpha-glucan branching enzyme activity glycosyltransferase activity transferase activity hexosyltransferase activity catalytic activity cation binding ion binding small molecule binding hydrolase activity, acting on glycosyl bonds hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity	metabolic process cellular process generation of precursor metabolites and energy regulation of biological process neuron apoptotic process regulation of cellular process negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process metabolic process cellular process generation of precursor metabolites and energy regulation of biological process neuron apoptotic process regulation of cellular process negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death regulation of neuron apoptotic process carbohydrate metabolic process glucan biosynthetic process polysaccharide biosynthetic process energy derivation by oxidation of organic compounds carbohydrate biosynthetic process glycogen metabolic process primary metabolic process glycogen biosynthetic process macromolecule biosynthetic process polysaccharide metabolic process glucan metabolic process biosynthetic process energy reserve metabolic process macromolecule metabolic process	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A, B, C	IPR006048	Alpha-amylase/branching enzyme, C-terminal all beta	Domain
A, B, C	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, C	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, B, C	IPR006047	Glycosyl hydrolase family 13, catalytic domain	Domain
A, B, C	IPR013780	Glycosyl hydrolase, all-beta	Homologous Superfamily
A, B, C	IPR037439	1,4-alpha-glucan-branching enzyme	Family
A, B, C	IPR004193	Glycoside hydrolase, family 13, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: Q04446	glycogen storage disease due to glycogen branching enzyme deficiency adult polyglucosan body disease glycogen storage disease peripheral neuropathy glycogen storage disease III hydrops fetalis inborn errors of metabolism Ketotic hypoglycemia ovarian cancer rhabdomyolysis attention deficit hyperactivity disorder, inattentive type cholestasis ductal breast carcinoma in situ glycogen storage disease due to glycogen branching enzyme deficiency, fatal perinatal neuromuscular form intellectual disability glycogen storage disease due to glycogen branching enzyme deficiency adult polyglucosan body disease glycogen storage disease peripheral neuropathy glycogen storage disease III hydrops fetalis inborn errors of metabolism Ketotic hypoglycemia ovarian cancer rhabdomyolysis attention deficit hyperactivity disorder, inattentive type cholestasis ductal breast carcinoma in situ glycogen storage disease due to glycogen branching enzyme deficiency, fatal perinatal neuromuscular form intellectual disability leukodystrophy pancreatic ductal adenocarcinoma plasma cell myeloma arthrogryposis subependymal giant cell astrocytoma breast carcinoma glioblastoma glycogen storage disease due to glycogen branching enzyme deficiency, childhood neuromuscular form IgA glomerulonephritis invasive ductal breast carcinoma lymphoplasmacytic lymphoma peripheral nervous system disease astrocytic tumor breast fibroadenoma glycogen storage disease due to glycogen branching enzyme deficiency, congenital neuromuscular form

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.