1VFM

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
Protein Family Annotation
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Alpha-amylase_N	e1vfmA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Alpha-amylase_N	ECOD (1.6)
A	Cyc-maltodext_C	e1vfmA2	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: Cyc-maltodext_C	ECOD (1.6)
A	Alpha-amylase	e1vfmA3	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Alpha-amylase	ECOD (1.6)
B	Alpha-amylase_N	e1vfmB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Alpha-amylase_N	ECOD (1.6)
B	Cyc-maltodext_C	e1vfmB2	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: Cyc-maltodext_C	ECOD (1.6)
B	Alpha-amylase	e1vfmB3	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Alpha-amylase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	PF02903	Alpha amylase, N-terminal ig-like domain (Alpha-amylase_N)	Alpha amylase, N-terminal ig-like domain	-	Domain
A, B	PF16657	Maltogenic Amylase, C-terminal domain (Malt_amylase_C)	Maltogenic Amylase, C-terminal domain	-	Family

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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR006047	Glycosyl hydrolase, family 13, catalytic domain	Domain
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	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.