3WN6 | pdb_00003wn6

Crystal structure of alpha-amylase AmyI-1 from Oryza sativa

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	(Trans)glycosidases	8098538	3000313	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8101008	3001528	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	(Trans)glycosidases	8098538	3000313	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8101008	3001528	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	(Trans)glycosidases	8098538	3000313	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8101008	3001528	SCOP2B (2022-06-29)
A	SCOP2 Family	Amylase, catalytic domain	8098537	4003138	SCOP2 (2022-06-29)
A	SCOP2 Family	alpha-Amylases, C-terminal beta-sheet domain	8101007	4002636	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	(Trans)glycosidases	8098538	3000313	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Glycosyl hydrolase domain-like	8101008	3001528	SCOP2 (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		e3wn6D1	A: DP domain	X: DP domain	H: DP domain	T: DUF5074	F:	ECOD (20:10:01)
C		e3wn6C1	A: DP domain	X: DP domain	H: DP domain	T: DUF5074	F:	ECOD (20:10:01)
B		e3wn6B1	A: DP domain	X: DP domain	H: DP domain	T: DUF5074	F:	ECOD (20:10:01)
A		e3wn6A1	A: DP domain	X: DP domain	H: DP domain	T: DUF5074	F:	ECOD (20:10:01)

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	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, D	PF07821	Alpha-amylase C-terminal beta-sheet domain (Alpha-amyl_C2)	Alpha-amylase C-terminal beta-sheet domain	This domain is organised as a five-stranded anti-parallel beta-sheet [1,2]. It is the probable result of a decay of the common-fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Alpha-amylase	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding hydrolase activity, acting on glycosyl bonds amylase activity alpha-amylase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity	carbohydrate metabolic process catabolic process glucan catabolic process carbohydrate catabolic process primary metabolic process macromolecule catabolic process polysaccharide metabolic process glucan metabolic process starch metabolic process polysaccharide catabolic process starch catabolic process metabolic process cellular process macromolecule metabolic process carbohydrate metabolic process catabolic process glucan catabolic process carbohydrate catabolic process primary metabolic process macromolecule catabolic process polysaccharide metabolic process glucan metabolic process starch metabolic process polysaccharide catabolic process starch catabolic process metabolic process cellular process macromolecule metabolic process sucrose catabolic process oligosaccharide catabolic process oligosaccharide metabolic process disaccharide metabolic process sucrose metabolic process disaccharide catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR012850	Alpha-amylase, C-terminal beta-sheet	Domain
A, B, C, D	IPR013775	Alpha-amylase, plant	Family
A, B, C, D	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A, B, C, D	IPR006047	Glycosyl hydrolase family 13, catalytic domain	Domain
A, B, C, D	IPR006046	Alpha amylase	Family
A, B, C, D	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.