2XJD

Crystal structure of the D52N variant of cytosolic 5'-nucleotidase II in complex with inorganic phosphate and deoxyadenosine triphosphate

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	HAD-like	8086277	3001890	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	5_nucleotid	e2xjdA1	A: alpha bundles	X: HAD superfamily helical bundle insertion domain	H: Insertion domain in cytosolic IMP-GMP specific 5'-nucleotidase (From Topology)	T: Insertion domain in cytosolic IMP-GMP specific 5'-nucleotidase	F: 5_nucleotid	ECOD (1.6)
A	5_nucleotid	e2xjdA2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: 5_nucleotid	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF05761	5' nucleotidase family (5_nucleotid)	5' nucleotidase family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	CYTOSOLIC PURINE 5'-NUCLEOTIDASE	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding phosphoric ester hydrolase activity nucleotidase activity hydrolase activity, acting on ester bonds XMP 5'-nucleosidase activity phosphatase activity hydrolase activity 5'-nucleotidase activity catalytic activity GMP 5'-nucleotidase activity IMP 5'-nucleotidase activity nucleobase-containing compound kinase activity nucleoside phosphotransferase activity kinase activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity ubiquitin-protein transferase activity cation binding metal ion binding identical protein binding protein binding	IMP metabolic process ribose phosphate metabolic process ribonucleotide catabolic process catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process purine ribonucleoside monophosphate catabolic process purine nucleoside monophosphate catabolic process nucleobase-containing compound metabolic process purine ribonucleoside monophosphate metabolic process purine nucleotide metabolic process organic substance metabolic process ribonucleotide metabolic process ribonucleoside monophosphate metabolic process IMP metabolic process ribose phosphate metabolic process ribonucleotide catabolic process catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process purine ribonucleoside monophosphate catabolic process purine nucleoside monophosphate catabolic process nucleobase-containing compound metabolic process purine ribonucleoside monophosphate metabolic process purine nucleotide metabolic process organic substance metabolic process ribonucleotide metabolic process ribonucleoside monophosphate metabolic process nucleobase-containing small molecule metabolic process purine nucleoside monophosphate metabolic process phosphate-containing compound metabolic process small molecule metabolic process ribonucleoside monophosphate catabolic process purine ribonucleotide catabolic process phosphorus metabolic process nucleoside monophosphate metabolic process nucleotide catabolic process nucleoside phosphate metabolic process organonitrogen compound catabolic process purine nucleotide catabolic process carbohydrate derivative catabolic process organonitrogen compound metabolic process nucleoside monophosphate catabolic process cellular metabolic process primary metabolic process purine-containing compound catabolic process nucleotide metabolic process organic cyclic compound catabolic process IMP catabolic process purine-containing compound metabolic process nucleobase-containing compound catabolic process organic cyclic compound metabolic process organophosphate metabolic process metabolic process cellular process purine ribonucleotide metabolic process organic substance catabolic process protein polyubiquitination protein ubiquitination macromolecule modification protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein K48-linked ubiquitination protein modification by small protein conjugation protein modification by small protein conjugation or removal deoxyribonucleotide metabolic process 2'-deoxyribonucleotide metabolic process purine deoxyribonucleoside monophosphate metabolic process deoxyribose phosphate metabolic process deoxyribonucleoside monophosphate metabolic process dGMP metabolic process purine deoxyribonucleotide metabolic process allantoin metabolic process amide metabolic process glycosyl compound metabolic process nucleoside metabolic process adenosine metabolic process purine nucleoside metabolic process ribonucleoside metabolic process purine ribonucleoside metabolic process regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms response to stimulus regulation of response to external stimulus negative regulation of response to biotic stimulus negative regulation of biological process response to biotic stimulus regulation of defense response to virus response to stress regulation of response to stress regulation of defense response to virus by host response to external biotic stimulus response to virus negative regulation of defense response to virus by host regulation of biological process response to other organism defense response negative regulation of response to stimulus biological regulation defense response to symbiont response to external stimulus defense response to virus regulation of response to stimulus defense response to other organism negative regulation of response to external stimulus negative regulation of defense response negative regulation of defense response to virus GMP metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR023214	HAD superfamily	Homologous Superfamily
A	IPR016695	Purine 5'-nucleotidase	Family
A	IPR036412	HAD-like superfamily	Homologous Superfamily
A	IPR008380	HAD-superfamily hydrolase, subfamily IG, 5'-nucleotidase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P49902	hereditary spastic paraplegia 45 hereditary spastic paraplegia pancreatic intraductal papillary-mucinous neoplasm Precursor Cell Lymphoblastic Leukemia Lymphoma systemic lupus erythematosus anorexia nervosa bipolar disorder cancer heart disease hypertensive disorder neurodegenerative disease pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia attention deficit hyperactivity disorder, inattentive type brain aneurysm hereditary spastic paraplegia 45 hereditary spastic paraplegia pancreatic intraductal papillary-mucinous neoplasm Precursor Cell Lymphoblastic Leukemia Lymphoma systemic lupus erythematosus anorexia nervosa bipolar disorder cancer heart disease hypertensive disorder neurodegenerative disease pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia attention deficit hyperactivity disorder, inattentive type brain aneurysm childhood acute lymphoblastic leukemia intellectual disability osteosarcoma pancreatic intraductal papillary-mucinous carcinoma paraplegia subependymal giant cell astrocytoma autism spectrum disorder breast cancer endogenous depression ovarian cancer

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.