2PAQ

Crystal structure of the 5'-deoxynucleotidase YfbR

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	d2paqa_	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	HD domain	5'-nucleotidase YfbR	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d2paqb_	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	HD domain	5'-nucleotidase YfbR	(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)
A	SCOP2 Family	HD domain-like	8031475	4000705	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	HD-domain/PDEase-like	8043853	3000943	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	HD-domain/PDEase-like	8043853	3000943	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	HD_3	e2paqA1	A: alpha complex topology	X: PDEase-like	H: HD-domain/PDEase-like (From Topology)	T: HD-domain/PDEase-like	F: HD_3	ECOD (1.6)
B	HD_3	e2paqB1	A: alpha complex topology	X: PDEase-like	H: HD-domain/PDEase-like (From Topology)	T: HD-domain/PDEase-like	F: HD_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.3210.10	Mainly Alpha	Orthogonal Bundle	Hypothetical protein af1432	Hypothetical protein af1432	CATH (4.3.0)
B	1.10.3210.10	Mainly Alpha	Orthogonal Bundle	Hypothetical protein af1432	Hypothetical protein af1432	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01966	HD domain (HD)	HD domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	5'-deoxynucleotidase YfbR	cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding phosphoric ester hydrolase activity 5'-deoxynucleotidase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity nucleoside phosphate binding cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding phosphoric ester hydrolase activity 5'-deoxynucleotidase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding identical protein binding protein binding nucleotidase activity thymidylate 5'-phosphatase activity 5'-nucleotidase activity	pyrimidine deoxyribonucleotide metabolic process nucleotide biosynthetic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process nucleobase-containing compound metabolic process deoxyribonucleotide biosynthetic process pyrimidine deoxyribonucleotide biosynthetic process phosphate-containing compound metabolic process organic substance biosynthetic process small molecule metabolic process phosphorus metabolic process nucleoside phosphate metabolic process pyrimidine-containing compound metabolic process pyrimidine deoxyribonucleotide metabolic process nucleotide biosynthetic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process nucleobase-containing compound metabolic process deoxyribonucleotide biosynthetic process pyrimidine deoxyribonucleotide biosynthetic process phosphate-containing compound metabolic process organic substance biosynthetic process small molecule metabolic process phosphorus metabolic process nucleoside phosphate metabolic process pyrimidine-containing compound metabolic process cellular metabolic process 2'-deoxyribonucleotide biosynthetic process primary metabolic process nucleotide metabolic process dUMP biosynthetic process deoxyribonucleoside monophosphate metabolic process dUMP metabolic process organic cyclic compound metabolic process biosynthetic process organophosphate biosynthetic process organic cyclic compound biosynthetic process nucleoside phosphate biosynthetic process metabolic process pyrimidine nucleoside monophosphate biosynthetic process deoxyribose phosphate biosynthetic process pyrimidine deoxyribonucleoside monophosphate metabolic process organic substance metabolic process deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process deoxyribonucleoside monophosphate biosynthetic process pyrimidine-containing compound biosynthetic process pyrimidine deoxyribonucleoside monophosphate biosynthetic process nucleoside monophosphate metabolic process carbohydrate derivative biosynthetic process pyrimidine nucleoside monophosphate metabolic process organonitrogen compound metabolic process 2'-deoxyribonucleotide metabolic process deoxyribose phosphate metabolic process nucleobase-containing compound biosynthetic process nucleoside monophosphate biosynthetic process organophosphate metabolic process cellular process pyrimidine nucleotide biosynthetic process pyrimidine-containing compound salvage pyrimidine nucleotide salvage nucleotide salvage cellular metabolic compound salvage pyrimidine deoxyribonucleotide salvage	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR003607	HD/PDEase domain	Domain
A, B	IPR022971	5'-deoxynucleotidase YfbR	Family
A, B	IPR006674	HD domain	Domain
A, B	IPR039356	5'-deoxynucleotidase YfbR/HDDC2	Family

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.