2WYI | pdb_00002wyi

Structure of the Streptococcus pyogenes family GH38 alpha-mannosidase complexed with swainsonine

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	AMS1_2nd	e2wyiB7	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: AMS1_2nd	ECOD (1.6)
B	AMS1_1st	e2wyiB6	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: AMS1_1st	ECOD (1.6)
B	Glyco_hydro_38C_1st	e2wyiB5	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich (From Topology)	T: supersandwich	F: Glyco_hydro_38C_1st	ECOD (1.6)
B	Alpha-mann_mid	e2wyiB4	A: alpha bundles	X: immunoglobulin/albumin-binding domain-like	H: Families 57/38 glycoside transferase middle domain (From Topology)	T: Families 57/38 glycoside transferase middle domain	F: Alpha-mann_mid	ECOD (1.6)
B	Glyco_hydro_38	e2wyiB3	A: a/b barrels	X: TIM beta/alpha-barrel	H: Glycoside hydrolase/deacetylase (From Topology)	T: Glycoside hydrolase/deacetylase	F: Glyco_hydro_38	ECOD (1.6)
A	AMS1_2nd	e2wyiA1	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: AMS1_2nd	ECOD (1.6)
A	AMS1_1st	e2wyiA5	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: AMS1_1st	ECOD (1.6)
A	Glyco_hydro_38C_1st	e2wyiA2	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich (From Topology)	T: supersandwich	F: Glyco_hydro_38C_1st	ECOD (1.6)
A	Alpha-mann_mid	e2wyiA4	A: alpha bundles	X: immunoglobulin/albumin-binding domain-like	H: Families 57/38 glycoside transferase middle domain (From Topology)	T: Families 57/38 glycoside transferase middle domain	F: Alpha-mann_mid	ECOD (1.6)
A	Glyco_hydro_38	e2wyiA3	A: a/b barrels	X: TIM beta/alpha-barrel	H: Glycoside hydrolase/deacetylase (From Topology)	T: Glycoside hydrolase/deacetylase	F: Glyco_hydro_38	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.11160	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	1.10.1240.90	Mainly Alpha	Orthogonal Bundle	Methyltransferase, Methionine Synthase (B12-binding Domains)	Chain A, domain 1	CATH (4.3.0)
B	1.20.1270.50	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)
B	2.60.40.2210	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
B	2.70.98.30	Mainly Beta	Distorted Sandwich	Beta-galactosidase	Chain A, domain 5	CATH (4.3.0)
B	2.60.40.2220	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
A	3.40.50.11160	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	1.10.1240.90	Mainly Alpha	Orthogonal Bundle	Methyltransferase, Methionine Synthase (B12-binding Domains)	Chain A, domain 1	CATH (4.3.0)
A	1.20.1270.50	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)
A	2.60.40.2210	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
A	2.70.98.30	Mainly Beta	Distorted Sandwich	Beta-galactosidase	Chain A, domain 5	CATH (4.3.0)
A	2.60.40.2220	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01074	Glycosyl hydrolases family 38 N-terminal domain (Glyco_hydro_38N)	Glycosyl hydrolases family 38 N-terminal domain	Glycosyl hydrolases are key enzymes of carbohydrate metabolism.	Domain
A, B	PF17677	Glycosyl hydrolases family 38 C-terminal beta sandwich domain (Glyco_hydro38C2)	Glycosyl hydrolases family 38 C-terminal beta sandwich domain	This domain is found at the C-terminal end of various glycosyl hydrolases belonging to family 38. The domain has a beta sandwich fold.	Domain
A, B	PF09261	Alpha mannosidase middle domain (Alpha-mann_mid)	Alpha mannosidase middle domain	Members of this family adopt a structure consisting of three alpha helices, in an immunoglobulin/albumin-binding domain-like fold. They are predominantly found in the enzyme alpha-mannosidase [1].	Domain
A, B	PF07748	Glycosyl hydrolases family 38 C-terminal domain (Glyco_hydro_38C)	Glycosyl hydrolases family 38 C-terminal domain	Glycosyl hydrolases are key enzymes of carbohydrate metabolism.	Domain
A, B	PF18438	Glycosyl hydrolases family 38 C-terminal domain 1 (Glyco_hydro_38)	Glycosyl hydrolases family 38 C-terminal domain 1	The enzymatic hydrolysis of alpha-mannosides is catalyzed by glycoside hydrolases (GH), termed alpha-mannosidases. Streptococcal (Sp) GH38 alpha-mannosidase active on N-glycans and possibly O-glycans. SpGH38 structure can be considered as five domain ...	The enzymatic hydrolysis of alpha-mannosides is catalyzed by glycoside hydrolases (GH), termed alpha-mannosidases. Streptococcal (Sp) GH38 alpha-mannosidase active on N-glycans and possibly O-glycans. SpGH38 structure can be considered as five domains: an N-terminal alpha/beta-domain, a three-helix bundle and three predominantly beta-sheet domains. This is the first of the three beta-sheet domains found in GH38, termed Beta-1. Structural analysis indicate that the beta-1 domain bows outward from the protein core, is involved in dimer interactions whilst also forming a lid 'above' and somewhat into the active centre of its dimer [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	ALPHA-MANNOSIDASE	binding carbohydrate binding hydrolase activity, acting on glycosyl bonds hydrolase activity, hydrolyzing O-glycosyl compounds mannosidase activity hydrolase activity alpha-mannosidase activity catalytic activity cation binding ion binding metal ion binding small molecule binding	monosaccharide metabolic process carbohydrate metabolic process mannose metabolic process hexose metabolic process small molecule metabolic process metabolic process cellular process primary metabolic process catabolic process oligosaccharide catabolic process oligosaccharide metabolic process carbohydrate catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR028995	Glycoside hydrolase families 57/38, central domain superfamily	Homologous Superfamily
A, B	IPR015341	Glycoside hydrolase family 38, central domain	Domain
A, B	IPR011330	Glycoside hydrolase/deacetylase, beta/alpha-barrel	Homologous Superfamily
A, B	IPR041509	Glycosyl hydrolases 38, beta-1 domain	Domain
A, B	IPR011682	Glycosyl hydrolase family 38, C-terminal	Domain
A, B	IPR041147	Glycosyl hydrolases family 38, C-terminal domain	Domain
A, B	IPR000602	Glycoside hydrolase family 38, N-terminal domain	Domain
A, B	IPR027291	Glycoside hydrolase 38, N-terminal domain superfamily	Homologous Superfamily
A, B	IPR011013	Galactose mutarotase-like domain superfamily	Homologous Superfamily
A, B	IPR037094	Glycoside hydrolase family 38, central domain superfamily	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.