3B9X | pdb_00003b9x

Crystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK in complex with inosine

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)
D	d3b9xd_	Alpha and beta proteins (a/b)	Nucleoside hydrolase	Nucleoside hydrolase	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d3b9xc_	Alpha and beta proteins (a/b)	Nucleoside hydrolase	Nucleoside hydrolase	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d3b9xb_	Alpha and beta proteins (a/b)	Nucleoside hydrolase	Nucleoside hydrolase	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d3b9xa_	Alpha and beta proteins (a/b)	Nucleoside hydrolase	Nucleoside hydrolase	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Nucleoside hydrolase	8039903	3001240	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleoside hydrolase	8039903	3001240	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleoside hydrolase	8039903	3001240	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleoside hydrolase	8039903	3001240	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)
D		e3b9xD1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: E1_dh	F:	ECOD (20:10:01)
C		e3b9xC1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: E1_dh	F:	ECOD (20:10:01)
B		e3b9xB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: E1_dh	F:	ECOD (20:10:01)
A		e3b9xA1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: E1_dh	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.90.245.10	Alpha Beta	Alpha-Beta Complex	Inosine-uridine Nucleoside N-ribohydrolase	Chain A	CATH (4.3.0)
C	3.90.245.10	Alpha Beta	Alpha-Beta Complex	Inosine-uridine Nucleoside N-ribohydrolase	Chain A	CATH (4.3.0)
B	3.90.245.10	Alpha Beta	Alpha-Beta Complex	Inosine-uridine Nucleoside N-ribohydrolase	Chain A	CATH (4.3.0)
A	3.90.245.10	Alpha Beta	Alpha-Beta Complex	Inosine-uridine Nucleoside N-ribohydrolase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01156	Inosine-uridine preferring nucleoside hydrolase (IU_nuc_hydro)	Inosine-uridine preferring nucleoside hydrolase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Pyrimidine-specific ribonucleoside hydrolase rihB	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding uridine nucleosidase activity hydrolase activity, acting on glycosyl bonds ribosylpyrimidine nucleosidase activity hydrolase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity purine nucleosidase activity identical protein binding cation binding ion binding binding calcium ion binding metal ion binding small molecule binding uridine nucleosidase activity hydrolase activity, acting on glycosyl bonds ribosylpyrimidine nucleosidase activity hydrolase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity purine nucleosidase activity identical protein binding protein binding	carbohydrate derivative catabolic process catabolic process purine nucleoside catabolic process carbohydrate derivative metabolic process primary metabolic process glycosyl compound catabolic process purine-containing compound catabolic process nucleoside metabolic process nucleobase-containing compound catabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process nucleobase-containing small molecule catabolic process nucleobase-containing small molecule metabolic process nucleoside catabolic process carbohydrate derivative catabolic process catabolic process purine nucleoside catabolic process carbohydrate derivative metabolic process primary metabolic process glycosyl compound catabolic process purine-containing compound catabolic process nucleoside metabolic process nucleobase-containing compound catabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process nucleobase-containing small molecule catabolic process nucleobase-containing small molecule metabolic process nucleoside catabolic process small molecule metabolic process metabolic process cellular process small molecule catabolic process purine nucleoside metabolic process pyrimidine-containing compound catabolic process pyrimidine nucleoside metabolic process pyrimidine-containing compound metabolic process pyrimidine nucleoside catabolic process pyrimidine ribonucleoside metabolic process pyrimidine ribonucleoside catabolic process ribonucleoside catabolic process ribonucleoside 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 pyrimidine nucleobase metabolic process nucleobase metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR023186	Inosine/uridine-preferring nucleoside hydrolase	Family
A, B, C, D	IPR001910	Inosine/uridine-preferring nucleoside hydrolase domain	Domain
A, B, C, D	IPR036452	Ribonucleoside hydrolase-like	Homologous Superfamily
A, B, C, D	IPR015910	Inosine/uridine-preferring nucleoside hydrolase, conserved site	Conserved Site
A, B, C, D	IPR022977	Pyrimidine-specific ribonucleoside hydrolase RihB	Family

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.