3W5N | pdb_00003w5n

Crystal Structure of Streptomyces avermitilis alpha-L-rhamnosidase complexed with L-rhamnose

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	SCOP2 Family	Bacterial alpha-L-rhamnosidase-like	8046910	4005365	SCOP2 (2022-06-29)
A	SCOP2 Family	Alpha-L-rhamnosidase C-terminal domain-like	8046914	4005366	SCOP2 (2022-06-29)
A	SCOP2 Family	alpha-L-rhamnosidase precatalytic domain-like	8047397	4005623	SCOP2 (2022-06-29)
A	SCOP2 Family	Alpha-L-rhamnosidase N-terminal domain-like	8050958	4007126	SCOP2 (2022-06-29)
A	SCOP2 Family	Alpha-L-rhamnosidase associated domain	8051886	4007570	SCOP2 (2022-06-29)
A	SCOP2 Family	E-set domains of sugar-utilizing enzymes	8051888	4007565	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Six-hairpin glycosidases	8051882	3000970	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	YicI C-terminal domain-like	8051884	3000267	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	galactose-binding domain-like	8051883	3000087	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Alpha-L-rhamnosidase associated domain -like	8051885	3002069	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Alpha-L-rhamnosidase associated domain -like	8051887	3002069	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	E set domains	8051889	3000070	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)
A	Bac_rhamnosid_N	e3w5nA3	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: Bac_rhamnosid_N	ECOD (1.6)
A	Bac_rhamnosid	e3w5nA6	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: Bac_rhamnosid	ECOD (1.6)
A	fn3_7	e3w5nA5	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: fn3_7	ECOD (1.6)
A	Bac_rhamnosid_C	e3w5nA2	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related (From Topology)	T: Glycoside hydrolase family 127 middle domain-related	F: Bac_rhamnosid_C	ECOD (1.6)
A	Bac_rhamnosid6H	e3w5nA1	A: alpha superhelices	X: Repetitive alpha hairpins	H: alpha/alpha toroid (From Topology)	T: alpha/alpha toroid	F: Bac_rhamnosid6H	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 (4.2.0)
A	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF05592	Bacterial alpha-L-rhamnosidase concanavalin-like domain (Bac_rhamnosid)	Bacterial alpha-L-rhamnosidase concanavalin-like domain	This family consists of bacterial rhamnosidase A and B enzymes. L-Rhamnose is abundant in biomass as a common constituent of glycolipids and glycosides, such as plant pigments, pectic polysaccharides, gums or biosurfactants. Some rhamnosides are impo ...	This family consists of bacterial rhamnosidase A and B enzymes. L-Rhamnose is abundant in biomass as a common constituent of glycolipids and glycosides, such as plant pigments, pectic polysaccharides, gums or biosurfactants. Some rhamnosides are important bioactive compounds. For example, terpenyl glycosides, the glycosidic precursor of aromatic terpenoids, act as important flavouring substances in grapes. Other rhamnosides act as cytotoxic rhamnosylated terpenoids, as signal substances in plants or play a role in the antigenicity of pathogenic bacteria [1].	Domain
A	PF08531	Alpha-L-rhamnosidase N-terminal domain (Bac_rhamnosid_N)	Alpha-L-rhamnosidase N-terminal domain	This family consists of bacterial rhamnosidase A and B enzymes. This domain is probably involved in substrate recognition.	Domain
A	PF25788	Rha78A-like, N-terminal immunoglobulin domain (Ig_Rha78A_N)	Rha78A-like, N-terminal immunoglobulin domain	This domain is found at the N-terminal end of Alpha-L-rhamnosidase from Streptomyces avermitilis (Rha78A) and similar proteins. Rha78A is able to degrade p-nitrophenyl-alpha-L-rhamnopyranoside in vitro. This domain adopts an immunoglobulin-like (Ig-l ...	This domain is found at the N-terminal end of Alpha-L-rhamnosidase from Streptomyces avermitilis (Rha78A) and similar proteins. Rha78A is able to degrade p-nitrophenyl-alpha-L-rhamnopyranoside in vitro. This domain adopts an immunoglobulin-like (Ig-like) fold.	Domain
A	PF17389	Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain (Bac_rhamnosid6H)	Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain	-	Repeat
A	PF17390	Bacterial alpha-L-rhamnosidase C-terminal domain (Bac_rhamnosid_C)	Bacterial alpha-L-rhamnosidase C-terminal domain	This family consists of bacterial rhamnosidase A and B enzymes. L-Rhamnose is abundant in biomass as a common constituent of glycolipids and glycosides, such as plant pigments, pectic polysaccharides, gums or biosurfactants. Some rhamnosides are impo ...	This family consists of bacterial rhamnosidase A and B enzymes. L-Rhamnose is abundant in biomass as a common constituent of glycolipids and glycosides, such as plant pigments, pectic polysaccharides, gums or biosurfactants. Some rhamnosides are important bioactive compounds. For example, terpenyl glycosides, the glycosidic precursor of aromatic terpenoids, act as important flavouring substances in grapes. Other rhamnosides act as cytotoxic rhamnosylated terpenoids, as signal substances in plants or play a role in the antigenicity of pathogenic bacteria [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Putative rhamnosidase	hydrolase activity, acting on glycosyl bonds alpha-L-rhamnosidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase 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	IPR053565	Glycosyl Hydrolase 78	Family
A	IPR008928	Six-hairpin glycosidase superfamily	Homologous Superfamily
A	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A	IPR012341	Six-hairpin glycosidase-like superfamily	Homologous Superfamily
A	IPR016007	Alpha-L-rhamnosidase	Family
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR035398	Alpha-L-rhamnosidase C-terminal domain	Domain
A	IPR035396	Alpha-L-rhamnosidase, six-hairpin glycosidase domain	Domain
A	IPR013737	Bacterial alpha-L-rhamnosidase N-terminal	Domain
A	IPR036116	Fibronectin type III superfamily	Homologous Superfamily
A	IPR008902	Alpha-L-rhamnosidase, concanavalin-like domain	Domain

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.