5D0F | pdb_00005d0f

Crystal Structure of the Candida Glabrata Glycogen Debranching Enzyme (E564Q) in complex with maltopentaose

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Six-hairpin glycosidases	8051878	3000970	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	(Trans)glycosidases	8051879	3000313	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8051880	3001528	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cupredoxins	8051881	3000886	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cupredoxins	8051881	3000886	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8051880	3001528	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	(Trans)glycosidases	8051879	3000313	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Six-hairpin glycosidases	8051878	3000970	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	hGDE_central_N	e5d0fA3	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: hGDE_central_N	ECOD (1.6)
A	hGDE_N	e5d0fA5	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: hGDE_N	ECOD (1.6)
A	hDGE_amylase	e5d0fA2	A: alpha arrays	X: Glycogen debranching enzyme (GDE) insertion domain (From Topology)	H: Glycogen debranching enzyme (GDE) insertion domain (From Topology)	T: Glycogen debranching enzyme (GDE) insertion domain	F: hDGE_amylase	ECOD (1.6)
A	hGDE_central_C	e5d0fA4	A: alpha bundles	X: Glycogen debranching enzyme (GDE) middle domain 2 (From Topology)	H: Glycogen debranching enzyme (GDE) middle domain 2 (From Topology)	T: Glycogen debranching enzyme (GDE) middle domain 2	F: hGDE_central_C	ECOD (1.6)
A	GDE_C	e5d0fA6	A: alpha superhelices	X: Repetitive alpha hairpins	H: alpha/alpha toroid (From Topology)	T: alpha/alpha toroid	F: GDE_C	ECOD (1.6)
A	Alpha-amylase	e5d0fA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Alpha-amylase	ECOD (1.6)
B	hGDE_central_N	e5d0fB6	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: hGDE_central_N	ECOD (1.6)
B	hGDE_N	e5d0fB2	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: hGDE_N	ECOD (1.6)
B	hDGE_amylase	e5d0fB3	A: alpha arrays	X: Glycogen debranching enzyme (GDE) insertion domain (From Topology)	H: Glycogen debranching enzyme (GDE) insertion domain (From Topology)	T: Glycogen debranching enzyme (GDE) insertion domain	F: hDGE_amylase	ECOD (1.6)
B	hGDE_central_C	e5d0fB1	A: alpha bundles	X: Glycogen debranching enzyme (GDE) middle domain 2 (From Topology)	H: Glycogen debranching enzyme (GDE) middle domain 2 (From Topology)	T: Glycogen debranching enzyme (GDE) middle domain 2	F: hGDE_central_C	ECOD (1.6)
B	GDE_C	e5d0fB4	A: alpha superhelices	X: Repetitive alpha hairpins	H: alpha/alpha toroid (From Topology)	T: alpha/alpha toroid	F: GDE_C	ECOD (1.6)
B	Alpha-amylase	e5d0fB5	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Alpha-amylase	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF14702	Central domain of human glycogen debranching enzyme (hGDE_central)	Central domain of human glycogen debranching enzyme	This is a central domain of the eukaryotic variant of the glycogen debranching enzyme (GDE). The eukaryotic GDE performs two functions: 4-alpha-D-glucanotransferase, EC:2.4.1.25, and Amylo-alpha-1,6-glucosidase, EC:3.2.1.33, performed by the, respect ...	This is a central domain of the eukaryotic variant of the glycogen debranching enzyme (GDE). The eukaryotic GDE performs two functions: 4-alpha-D-glucanotransferase, EC:2.4.1.25, and Amylo-alpha-1,6-glucosidase, EC:3.2.1.33, performed by the, respectively N- and C- terminal halves of eukaryotic GDE enzyme This central domain follows the glucanotransferase domain and precedes the glucosidase (GDE_N) domain. It is very likely that the current definition contains two or more domains, by analogy with bacterial GDEs, this domain should be involved in substrate- binding either for the N-terminal glucanotransferase and/or the the C-terminal glucosidase (or both).	Domain
A, B	PF06202	Amylo-alpha-1,6-glucosidase (GDE_C)	Amylo-alpha-1,6-glucosidase	-	Repeat
A, B	PF14699	N-terminal domain from the human glycogen debranching enzyme (hGDE_N)	N-terminal domain from the human glycogen debranching enzyme	-	Family
A, B	PF14701	Glycogen debranching enzyme, glucanotransferase domain (hDGE_amylase)	Glycogen debranching enzyme, glucanotransferase domain	This is a glucanotransferase catalytic domain of the eukaryotic variant of the glycogen debranching enzyme (GDE). The eukaryotic GDEs performs two functions: 4-alpha-D-glucanotransferase, EC:2.4.1.25, and Amylo-alpha-1,6-glucosidase, EC:3.2.1.33, per ...	This is a glucanotransferase catalytic domain of the eukaryotic variant of the glycogen debranching enzyme (GDE). The eukaryotic GDEs performs two functions: 4-alpha-D-glucanotransferase, EC:2.4.1.25, and Amylo-alpha-1,6-glucosidase, EC:3.2.1.33, performed by the, respectively N- and C- terminal halves of eukaryotic GDE enzymes. The domain is a catalytic domain responsible for the glucanotransferase function. It belongs to the alpha-amylase clan and is predicted to have a structure of a 8-stranded alpha/beta barrel (TIM barrel) where strands are interrupted by long loops and additional mini-domains. In most other amylases, the catalytic domain is followed by a beta- barrel substrate binding domain, but presence of such a domain cannot be verified in the human (and other eukaryotic) GDE enzymes.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Uncharacterized protein	alpha-glucosidase activity hydrolase activity, acting on glycosyl bonds glucosidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity amylo-alpha-1,6-glucosidase activity glycosyltransferase activity 4-alpha-glucanotransferase activity transferase activity hexosyltransferase activity	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 generation of precursor metabolites and energy glycogen biosynthetic process macromolecule biosynthetic process polysaccharide metabolic process glucan metabolic process biosynthetic process metabolic 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 generation of precursor metabolites and energy glycogen biosynthetic process macromolecule biosynthetic process polysaccharide metabolic process glucan metabolic process biosynthetic process metabolic process cellular process energy reserve metabolic process macromolecule metabolic process catabolic process glucan catabolic process carbohydrate catabolic process macromolecule catabolic process glycogen catabolic process polysaccharide catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR008928	Six-hairpin glycosidase superfamily	Homologous Superfamily
A, B	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A, B	IPR029436	Eukaryotic glycogen debranching enzyme, N-terminal domain	Domain
A, B	IPR012341	Six-hairpin glycosidase-like superfamily	Homologous Superfamily
A, B	IPR010401	Glycogen debranching enzyme	Family
A, B	IPR032788	Glycogen debranching enzyme, central domain	Domain
A, B	IPR032792	Glycogen debranching enzyme, glucanotransferase domain	Domain
A, B	IPR006421	Glycogen debranching enzyme, metazoa	Family
A, B	IPR032790	Glycogen debranching enzyme, C-terminal	Domain

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.