2VKQ

Crystal structure of human cytosolic 5'-nucleotidase III (cN-III, NT5C3) in complex with beryllium trifluoride

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
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2vkqa_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	Pyrimidine 5'-nucleotidase (UMPH-1)	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Pyrimidine 5'-nucleotidase (UMPH-1)	8025160	4002703	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	HAD-like	8037539	3001890	SCOP2 (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	UMPH-1	e2vkqA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: UMPH-1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
A	1.10.150.340	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF05822	Pyrimidine 5'-nucleotidase (UMPH-1) (UMPH-1)	Pyrimidine 5'-nucleotidase (UMPH-1)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	CYTOSOLIC 5'-NUCLEOTIDASE III	cation binding magnesium ion binding ion binding binding metal ion 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 cation binding magnesium ion binding ion binding binding metal ion 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 nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid tRNA 2'-phosphotransferase activity catalytic activity, acting on a tRNA transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups	organonitrogen compound metabolic process glycosyl compound metabolic process pyrimidine-containing compound metabolic process carbohydrate derivative metabolic process primary metabolic process pyrimidine nucleoside metabolic process nucleoside metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process nucleobase-containing small molecule metabolic process small molecule metabolic process metabolic process nucleoside phosphate metabolic process organonitrogen compound metabolic process glycosyl compound metabolic process pyrimidine-containing compound metabolic process carbohydrate derivative metabolic process primary metabolic process pyrimidine nucleoside metabolic process nucleoside metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process nucleobase-containing small molecule metabolic process small molecule metabolic process metabolic process nucleoside phosphate metabolic process cellular metabolic process nucleotide metabolic process organophosphate metabolic process phosphate-containing compound metabolic process cellular process phosphorus metabolic process biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to virus defense response to other organism response to stress response to external biotic stimulus response to virus	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear body intracellular organelle nucleoplasm organelle lumen organelle intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen endoplasmic reticulum endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR023214	HAD superfamily	Homologous Superfamily
A	IPR036412	HAD-like superfamily	Homologous Superfamily
A	IPR006434	Pyrimidine 5'-nucleotidase, eukaryotic	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9H0P0	hemolytic anemia due to pyrimidine 5' nucleotidase deficiency Chloracne congenital nonspherocytic hemolytic anemia psoriasis congenital anemia intellectual disability

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.