2XPK | pdb_00002xpk

Cell-penetrant, nanomolar O-GlcNAcase inhibitors selective against lysosomal hexosaminidases

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	d2xpkb3	All alpha proteins	Hyaluronidase domain-like	Hyaluronidase post-catalytic domain-like	automated matches	automated matches	(Clostridium perfringens ) [TaxId: 1502 ],	SCOPe (2.08)
B	d2xpkb2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	alpha-D-glucuronidase/Hyaluronidase catalytic domain	automated matches	(Clostridium perfringens ) [TaxId: 1502 ],	SCOPe (2.08)
B	d2xpkb1	Alpha and beta proteins (a+b)	Zincin-like	beta-N-acetylhexosaminidase-like domain	automated matches	automated matches	(Clostridium perfringens ) [TaxId: 1502 ],	SCOPe (2.08)
A	d2xpka3	All alpha proteins	Hyaluronidase domain-like	Hyaluronidase post-catalytic domain-like	automated matches	automated matches	(Clostridium perfringens ) [TaxId: 1502 ],	SCOPe (2.08)
A	d2xpka2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	alpha-D-glucuronidase/Hyaluronidase catalytic domain	automated matches	(Clostridium perfringens ) [TaxId: 1502 ],	SCOPe (2.08)
A	d2xpka1	Alpha and beta proteins (a+b)	Zincin-like	beta-N-acetylhexosaminidase-like domain	automated matches	automated matches	(Clostridium perfringens ) [TaxId: 1502 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	(Trans)glycosidases	8038623	3000313	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	beta-N-acetylhexosaminidase-like domain	8038626	3000192	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Hyaluronidase post-catalytic domain-like	8038622	3001475	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	beta-N-acetylhexosaminidase-like domain	8038626	3000192	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	(Trans)glycosidases	8038623	3000313	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Hyaluronidase post-catalytic domain-like	8038622	3001475	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)
B	NagJ_C	e2xpkB1	A: alpha bundles	X: Hyaluronidase domain-like	H: Hyaluronidase post-catalytic domain-like (From Topology)	T: Hyaluronidase post-catalytic domain-like	F: NagJ_C	ECOD (1.6)
B	NAGidase	e2xpkB2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: NAGidase	ECOD (1.6)
B	Glyco_hydro_20b	e2xpkB3	A: mixed a+b and a/b	X: Zincin-like	H: beta-N-acetylhexosaminidase-like domain (From Topology)	T: beta-N-acetylhexosaminidase-like domain	F: Glyco_hydro_20b	ECOD (1.6)
A	NagJ_C	e2xpkA1	A: alpha bundles	X: Hyaluronidase domain-like	H: Hyaluronidase post-catalytic domain-like (From Topology)	T: Hyaluronidase post-catalytic domain-like	F: NagJ_C	ECOD (1.6)
A	NAGidase	e2xpkA2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: NAGidase	ECOD (1.6)
A	Glyco_hydro_20b	e2xpkA3	A: mixed a+b and a/b	X: Zincin-like	H: beta-N-acetylhexosaminidase-like domain (From Topology)	T: beta-N-acetylhexosaminidase-like domain	F: Glyco_hydro_20b	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.379.10	Alpha Beta	2-Layer Sandwich	Chitobiase	domain 2	CATH (4.3.0)
B	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
B	1.20.58.460	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
A	3.30.379.10	Alpha Beta	2-Layer Sandwich	Chitobiase	domain 2	CATH (4.3.0)
A	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
A	1.20.58.460	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	O-GLCNACASE NAGJ	binding carbohydrate binding hydrolase activity, acting on glycosyl bonds hexosaminidase activity beta-N-acetylhexosaminidase activity beta-N-acetylglucosaminidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity catalytic activity, acting on a protein	carbohydrate metabolic process primary metabolic process metabolic process cellular process macromolecule modification protein deglycosylation carbohydrate derivative metabolic process protein metabolic process macromolecule metabolic process protein modification process glycoprotein metabolic process polysaccharide metabolic process catabolic process polysaccharide catabolic process carbohydrate metabolic process primary metabolic process metabolic process cellular process macromolecule modification protein deglycosylation carbohydrate derivative metabolic process protein metabolic process macromolecule metabolic process protein modification process glycoprotein metabolic process polysaccharide metabolic process catabolic process polysaccharide catabolic process carbohydrate catabolic process macromolecule catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR051822	Glycosyl Hydrolase Family 84	Family
A, B	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A, B	IPR003961	Fibronectin type III	Domain
A, B	IPR029018	Beta-hexosaminidase-like, domain 2	Homologous Superfamily
A, B	IPR011496	Beta-N-acetylglucosaminidase, catalytic domain	Domain
A, B	IPR008965	CBM2/CBM3, carbohydrate-binding domain superfamily	Homologous Superfamily
A, B	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A, B	IPR002102	Cellulosome anchoring protein, cohesin domain	Domain
A, B	IPR000421	Coagulation factor 5/8, C-terminal domain	Domain
A, B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B	IPR015882	Beta-hexosaminidase, bacterial type, N-terminal	Domain
A, B	IPR049019	NagJ-like, helical domain	Domain
A, B	IPR036116	Fibronectin type III 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.