2XVK

crystal structure of alpha-xylosidase (GH31) from Cellvibrio japonicus in complex with 5-fluoro-alpha-D-xylopyranosyl fluoride

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	d2xvka1	All beta proteins	Supersandwich	Galactose mutarotase-like	Glycosyl hydrolase family 31, N-terminal domain-like	Alpha-xylosidase	(Cellvibrio japonicus ) [TaxId: 155077 ],	SCOPe (2.08)
A	d2xvka4	All beta proteins	Glycosyl hydrolase domain	Glycosyl hydrolase domain	Glycosyl hydrolase family 31, domain 3	Alpha-xylosidase	(Cellvibrio japonicus ) [TaxId: 155077 ],	SCOPe (2.08)
A	d2xvka5	All beta proteins	Glycolsyl hydrolase family 31 C-terminal domain-like	Glycolsyl hydrolase family 31 C-terminal domain	Glycolsyl hydrolase family 31 C-terminal domain	Alpha-xylosidase, C-terminal domain	(Cellvibrio japonicus ) [TaxId: 155077 ],	SCOPe (2.08)
A	d2xvka2	All beta proteins	Anthrax protective antigen N-terminal-like	PA14-like	Glycoside hydrolase family 31 (GH31), PA14-like domain	Alpha-xylosidase	(Cellvibrio japonicus ) [TaxId: 155077 ],	SCOPe (2.08)
A	d2xvka3	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	Glycosyl hydrolase family 31 catalytic domain	Catalytic domain of alpha-xylosidase	(Cellvibrio japonicus ) [TaxId: 155077 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	YicI C-terminal domain-like	8090415	3000267	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	galactose-binding domain-like	8090417	3000087	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Galactose mutarotase-like	8090414	3000035	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Galactose mutarotase-like	8090414	3000035	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	(Trans)glycosidases	8090419	3000313	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8090421	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	Glyco_hydro_31_C	e2xvkA2	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: Glyco_hydro_31_C	ECOD (1.6)
A	Gal_mutarotas_2	e2xvkA3	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich (From Topology)	T: supersandwich	F: Gal_mutarotas_2	ECOD (1.6)
A	DUF5110	e2xvkA4	A: beta sandwiches	X: Putative glucosidase YicI, C-terminal domain (From Topology)	H: Putative glucosidase YicI, C-terminal domain (From Topology)	T: Putative glucosidase YicI, C-terminal domain	F: DUF5110	ECOD (1.6)
A	PA14	e2xvkA1	A: beta sandwiches	X: N-terminal beta-sandwich domain in anthrax protective antigen (From Topology)	H: N-terminal beta-sandwich domain in anthrax protective antigen (From Topology)	T: N-terminal beta-sandwich domain in anthrax protective antigen	F: PA14	ECOD (1.6)
A	Glyco_hydro_31_N	e2xvkA5	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glyco_hydro_31_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.1760	Mainly Beta	Sandwich	Immunoglobulin-like	glycosyl hydrolase (family 31)	CATH (4.3.0)
A	2.60.120.380	Mainly Beta	Sandwich	Jelly Rolls		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	PF21365	Glycosyl hydrolase family 31 C-terminal domain (Glyco_hydro_31_3rd)	Glycosyl hydrolase family 31 C-terminal domain	Glycosyl hydrolases are key enzymes of carbohydrate metabolism. Family 31 comprises of enzymes that are, or similar to, alpha- galactosidases. This entry represents the 3rd beta sandwich domain.	Domain
A	PF13802	Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain (Gal_mutarotas_2)	Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain	This entry represents the first of three common domains found in Glycosyl hydrolase 31 family proteins. It has a galactose mutarotase superfamily fold.	Domain
A	PF17137	Domain of unknown function (DUF5110) (DUF5110)	Domain of unknown function (DUF5110)	-	Family
A	PF01055	Glycosyl hydrolases family 31 TIM-barrel domain (Glyco_hydro_31_2nd)	Glycosyl hydrolases family 31 TIM-barrel domain	Glycosyl hydrolases are key enzymes of carbohydrate metabolism. Family 31 comprises of enzymes that are, or similar to, alpha- galactosidases. This entry corresponds to the second domain of family 31 enzymes and adopts a TIM-barrel fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	ALPHA-XYLOSIDASE, PUTATIVE, XYL31A	binding carbohydrate binding hydrolase activity, acting on glycosyl bonds hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity	carbohydrate metabolic process primary metabolic process metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000322	Glycoside hydrolase family 31, TIM barrel domain	Domain
A	IPR048395	Glycosyl hydrolase family 31, C-terminal domain	Domain
A	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A	IPR051816	Glycosyl Hydrolase Family 31	Family
A	IPR033403	Domain of unknown function DUF5110	Domain
A	IPR011658	PA14 domain	Domain
A	IPR037524	PA14/GLEYA domain	Domain
A	IPR013780	Glycosyl hydrolase, all-beta	Homologous Superfamily
A	IPR025887	Glycoside hydrolase family 31, N-terminal domain	Domain
A	IPR011013	Galactose mutarotase-like 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.