4FNS | pdb_00004fns

Crystal structure of GH36 alpha-galactosidase AgaA A355E from Geobacillus stearothermophilus in complex with 1-deoxygalactonojirimycin

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)
A	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8093328	3001528	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Galactose mutarotase-like	8093329	3000035	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	(Trans)glycosidases	8093330	3000313	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	(Trans)glycosidases	8093330	3000313	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Galactose mutarotase-like	8093329	3000035	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8093328	3001528	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8093328	3001528	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	(Trans)glycosidases	8093330	3000313	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Galactose mutarotase-like	8093329	3000035	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	(Trans)glycosidases	8093330	3000313	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8093328	3001528	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Galactose mutarotase-like	8093329	3000035	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	Glyco_hydro_36C	e4fnsA2	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: Glyco_hydro_36C	ECOD (1.6)
A	Glyco_hydro_36N	e4fnsA3	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich (From Topology)	T: supersandwich	F: Glyco_hydro_36N	ECOD (1.6)
A	Melibiase	e4fnsA4	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Melibiase	ECOD (1.6)
B	Glyco_hydro_36C	e4fnsB1	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: Glyco_hydro_36C	ECOD (1.6)
B	Glyco_hydro_36N	e4fnsB3	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich (From Topology)	T: supersandwich	F: Glyco_hydro_36N	ECOD (1.6)
B	Melibiase	e4fnsB2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Melibiase	ECOD (1.6)
C	Glyco_hydro_36C	e4fnsC1	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: Glyco_hydro_36C	ECOD (1.6)
C	Glyco_hydro_36N	e4fnsC3	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich (From Topology)	T: supersandwich	F: Glyco_hydro_36N	ECOD (1.6)
C	Melibiase	e4fnsC4	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Melibiase	ECOD (1.6)
D	Glyco_hydro_36C	e4fnsD1	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: Glyco_hydro_36C	ECOD (1.6)
D	Glyco_hydro_36N	e4fnsD3	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich (From Topology)	T: supersandwich	F: Glyco_hydro_36N	ECOD (1.6)
D	Melibiase	e4fnsD4	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Melibiase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.70.98.60	Mainly Beta	Distorted Sandwich	Beta-galactosidase	Chain A, domain 5	CATH (4.3.0)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	2.60.40.1180	Mainly Beta	Sandwich	Immunoglobulin-like	Golgi alpha-mannosidase II	CATH (4.3.0)
B	2.70.98.60	Mainly Beta	Distorted Sandwich	Beta-galactosidase	Chain A, domain 5	CATH (4.3.0)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
B	2.60.40.1180	Mainly Beta	Sandwich	Immunoglobulin-like	Golgi alpha-mannosidase II	CATH (4.3.0)
C	2.70.98.60	Mainly Beta	Distorted Sandwich	Beta-galactosidase	Chain A, domain 5	CATH (4.3.0)
C	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
C	2.60.40.1180	Mainly Beta	Sandwich	Immunoglobulin-like	Golgi alpha-mannosidase II	CATH (4.3.0)
D	2.70.98.60	Mainly Beta	Distorted Sandwich	Beta-galactosidase	Chain A, domain 5	CATH (4.3.0)
D	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
D	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	PF02065	Melibiase (Melibiase)	Melibiase	-	Family
A, B, C, D	PF16875	Glycosyl hydrolase family 36 N-terminal domain (Glyco_hydro_36N)	Glycosyl hydrolase family 36 N-terminal domain	This domain is found at the N-terminus of many family 36 glycoside hydrolases. It has a beta-supersandwich fold [1].	Domain
A, B, C, D	PF16874	Glycosyl hydrolase family 36 C-terminal domain (Glyco_hydro_36C)	Glycosyl hydrolase family 36 C-terminal domain	This domain is found at the C-terminus of many family 36 glycoside hydrolases. It has a beta-sandwich structure with a Greek key motif [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Alpha-galactosidase AgaA	alpha-galactosidase activity hydrolase activity, acting on glycosyl bonds hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity galactosidase activity	carbohydrate metabolic process catabolic process oligosaccharide catabolic process oligosaccharide metabolic process raffinose catabolic process carbohydrate catabolic process primary metabolic process metabolic process cellular process raffinose metabolic process protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis carbohydrate metabolic process catabolic process oligosaccharide catabolic process oligosaccharide metabolic process raffinose catabolic process carbohydrate catabolic process primary metabolic process metabolic process cellular process raffinose metabolic process protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis stachyose metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR031704	Glycosyl hydrolase family 36, N-terminal	Domain
A, B, C, D	IPR031705	Glycosyl hydrolase family 36, C-terminal	Domain
A, B, C, D	IPR050985	Alpha-glycosidase and related enzymes	Family
A, B, C, D	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A, B, C, D	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B, C, D	IPR000111	Glycoside hydrolase family 27/36, conserved site	Conserved Site
A, B, C, D	IPR038417	Alpha-galactosidase, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR002252	Glycoside hydrolase family 36	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.