1VFM | pdb_00001vfm

Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase 2/alpha-cyclodextrin complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1vfmb1	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	automated matches	automated matches	(Thermoactinomyces vulgaris ) [TaxId: 2026 ],	SCOPe (2.08)
B	d1vfmb2	All beta proteins	Glycosyl hydrolase domain	Glycosyl hydrolase domain	automated matches	automated matches	(Thermoactinomyces vulgaris ) [TaxId: 2026 ],	SCOPe (2.08)
B	d1vfmb3	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	Amylase, catalytic domain	automated matches	(Thermoactinomyces vulgaris ) [TaxId: 2026 ],	SCOPe (2.08)
A	d1vfma1	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	automated matches	automated matches	(Thermoactinomyces vulgaris ) [TaxId: 2026 ],	SCOPe (2.08)
A	d1vfma2	All beta proteins	Glycosyl hydrolase domain	Glycosyl hydrolase domain	automated matches	automated matches	(Thermoactinomyces vulgaris ) [TaxId: 2026 ],	SCOPe (2.08)
A	d1vfma3	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	Amylase, catalytic domain	automated matches	(Thermoactinomyces vulgaris ) [TaxId: 2026 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	E set domains	8054927	3000070	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	(Trans)glycosidases	8033456	3000313	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8033454	3001528	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	E set domains	8054927	3000070	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	(Trans)glycosidases	8033456	3000313	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8033454	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)
B	Copper-bind	e1vfmB1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (develop294)
B	Alpha-L-AF_C	e1vfmB2	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Alpha-L-AF_C	ECOD (develop294)
B	Alpha-amylase	e1vfmB3	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Alpha-amylase	ECOD (develop294)
A	Copper-bind	e1vfmA1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (develop294)
A	Alpha-L-AF_C	e1vfmA2	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Alpha-L-AF_C	ECOD (develop294)
A	Alpha-amylase	e1vfmA3	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Alpha-amylase	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
B	3.90.400.10	Alpha Beta	Alpha-Beta Complex	Oligo-1,6-glucosidase	domain 2	CATH (4.3.0)
B	2.60.40.1180	Mainly Beta	Sandwich	Immunoglobulin-like	Golgi alpha-mannosidase II	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
A	3.90.400.10	Alpha Beta	Alpha-Beta Complex	Oligo-1,6-glucosidase	domain 2	CATH (4.3.0)
A	2.60.40.1180	Mainly Beta	Sandwich	Immunoglobulin-like	Golgi alpha-mannosidase II	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Neopullulanase 2	hydrolase activity, acting on glycosyl bonds hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity neopullulanase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	carbohydrate metabolic process primary metabolic process metabolic process cellular process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR045857	Oligo-1,6-glucosidase, domain 2	Homologous Superfamily
A, B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, B	IPR004185	Glycoside hydrolase, family 13, N-terminal Ig-like domain	Domain
A, B	IPR032091	Maltogenic amylase-like, C-terminal	Domain
A, B	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A, B	IPR006047	Glycosyl hydrolase family 13, catalytic domain	Domain
A, B	IPR013780	Glycosyl hydrolase, all-beta	Homologous Superfamily

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.