1Q91

Crystal structure of human mitochondrial deoxyribonucleotidase in complex with the inhibitor DPB-T

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1q91a_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	5'(3')-deoxyribonucleotidase (dNT-2)	5'(3')-deoxyribonucleotidase (dNT-2)	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	SCOP2B Superfamily	HAD-like	8039928	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	NT5C	e1q91A1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: NT5C	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	1.10.40.40	Mainly Alpha	Orthogonal Bundle	Ribonucleotide Reductase Protein R1	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF06941	5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C) (NT5C)	5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	5(3)-deoxyribonucleotidase	phosphoric ester hydrolase activity nucleotidase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity 5'-nucleotidase activity binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding cation binding phosphoric ester hydrolase activity nucleotidase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity 5'-nucleotidase activity binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding cation binding ion binding metal ion binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process pyrimidine deoxyribonucleotide catabolic process pyrimidine deoxyribonucleoside monophosphate catabolic process catabolic process deoxyribonucleoside monophosphate catabolic process deoxyribonucleotide catabolic process pyrimidine deoxyribonucleotide metabolic process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process pyrimidine deoxyribonucleotide catabolic process pyrimidine deoxyribonucleoside monophosphate catabolic process catabolic process deoxyribonucleoside monophosphate catabolic process deoxyribonucleotide catabolic process pyrimidine deoxyribonucleotide metabolic process pyrimidine-containing compound catabolic process organophosphate catabolic process carbohydrate derivative metabolic process nucleoside phosphate catabolic process deoxyribose phosphate catabolic process pyrimidine nucleotide metabolic process pyrimidine deoxyribonucleoside monophosphate metabolic process pyrimidine nucleotide catabolic process deoxyribonucleotide metabolic process dUMP catabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process nucleoside monophosphate metabolic process phosphorus metabolic process nucleotide catabolic process pyrimidine nucleoside monophosphate catabolic process nucleoside phosphate metabolic process pyrimidine nucleoside monophosphate metabolic process carbohydrate derivative catabolic process nucleoside monophosphate catabolic process pyrimidine-containing compound metabolic process 2'-deoxyribonucleotide metabolic process nucleotide metabolic process deoxyribose phosphate metabolic process deoxyribonucleoside monophosphate metabolic process dUMP metabolic process nucleobase-containing compound catabolic process organophosphate metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR010708	5'(3')-deoxyribonucleotidase	Family
A	IPR036412	HAD-like superfamily	Homologous Superfamily
A	IPR023214	HAD superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9NPB1	osteosarcoma

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	5'-nucleotidase (mitochondrial) M-CSA #812	Mitochondrial 5'-(3') deoxyribonucleotidase (dNT-2) dephosphorylates thymidine and deoxyuridine monophosphates, thus regulates the precursors for mitochondrial DNA synthesis and protects mitochondrial DNA replication from excess dTTP.	Defined by 3 residues: ASP:A-10 [auth A-41]ASP:A-12 [auth A-43]ASP:A-145 [auth A-176] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.1.3.5 (PDB Primary Data) Search M-CSA Motif + EC 3.1.3.5 EC: 3.1.3 (UniProt) Search M-CSA Motif + EC 3.1.3

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.