4KXL | pdb_00004kxl

Crystal structure of DNPH1 (RCL) with 6-CYCLOPENTYL-AMP

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Ribosomal_S13_N	e4kxlA1	A: a/b three-layered sandwiches	X: DEATH domain	H: 40S ribosomal protein S13 N-terminal domain	T: 40S ribosomal protein S13 N-terminal domain	F: Ribosomal_S13_N	ECOD (v294.1)
B	Ribosomal_S4e	e4kxlB1	A: a/b three-layered sandwiches	X: jelly-roll	H: Galactose-binding domain-like	T: Galactose-binding domain-like	F: Ribosomal_S4e	ECOD (v294.1)
C	DUF4170	e4kxlC1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: DUF4170	ECOD (v294.1)
D	Acylphosphatase	e4kxlD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: Acylphosphatase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
C	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
D	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF05014	Nucleoside 2-deoxyribosyltransferase (Nuc_deoxyrib_tr)	Nucleoside 2-deoxyribosyltransferase	Nucleoside 2-deoxyribosyltransferase EC:2.4.2.6 catalyses the cleavage of the glycosidic bonds of 2`-deoxyribonucleosides [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	2'-deoxynucleoside 5'-phosphate N-hydrolase 1	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity hydrolase activity, acting on glycosyl bonds hydrolase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity 5-hydroxymethyl-dUMP N-hydrolase activity	regulation of growth regulation of biological process regulation of cellular process regulation of cellular component organization biological regulation growth positive regulation of biological process positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular process cellular component organization or biogenesis regulation of growth regulation of biological process regulation of cellular process regulation of cellular component organization biological regulation growth positive regulation of biological process positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular process cellular component organization or biogenesis positive regulation of cellular process nucleoside phosphate metabolic process deoxyribonucleoside monophosphate catabolic process nucleoside monophosphate catabolic process catabolic process organophosphate catabolic process primary metabolic process nucleoside phosphate catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process metabolic process small molecule metabolic process phosphorus metabolic process nucleoside monophosphate metabolic process carbohydrate derivative biosynthetic process glycosyl compound biosynthetic process small molecule biosynthetic process nucleoside salvage carbohydrate derivative metabolic process nucleoside biosynthetic process nucleobase-containing compound biosynthetic process nucleoside metabolic process nucleobase-containing small molecule biosynthetic process metabolic compound salvage biosynthetic process allantoin metabolic process developmental process epithelium development cellular developmental process cell differentiation anatomical structure development tissue development epithelial cell differentiation dGMP catabolic process purine deoxyribonucleoside monophosphate catabolic process deoxyribose phosphate catabolic process purine nucleoside monophosphate catabolic process purine nucleotide metabolic process purine nucleoside monophosphate metabolic process nucleotide catabolic process purine nucleotide catabolic process purine deoxyribonucleotide catabolic process carbohydrate derivative catabolic process 2'-deoxyribonucleotide metabolic process purine deoxyribonucleoside monophosphate metabolic process purine-containing compound catabolic process nucleotide metabolic process purine-containing compound metabolic process dGMP metabolic process purine deoxyribonucleotide metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR007710	Nucleoside 2-deoxyribosyltransferase	Family
A, B, C, D	IPR051239	2'-Deoxynucleoside 5'-phosphate N-hydrolase	Family
A, B, C, D	IPR028607	2-deoxynucleoside 5-phosphate N-hydrolase 1, DNPH1	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.