4YIH | pdb_00004yih

Crystal structure of human cytosolic 5'(3')-deoxyribonucleotidase in complex with the inhibitor PB-PVU

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d4yiha_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	5'(3')-deoxyribonucleotidase (dNT-2)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4yihb_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	5'(3')-deoxyribonucleotidase (dNT-2)	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	SCOP2B Superfamily	HAD-like	8088995	3001890	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HAD-like	8088995	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		e4yihA1	A: Flavodoxin-like	X: Class I glutamine amidotransferase-like	H: RNA polymerase I subunits A49/A34.5 dimerization domains	T:	F:	ECOD (20:10:01)
B		e4yihB1	A: Flavodoxin-like	X: Class I glutamine amidotransferase-like	H: RNA polymerase I subunits A49/A34.5 dimerization domains	T:	F:	ECOD (20:10:01)

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)
B	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
B	1.10.40.40	Mainly Alpha	Orthogonal Bundle	Ribonucleotide Reductase Protein R1	domain 1	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	5'(3')-deoxyribonucleotidase, cytosolic type	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 nucleotide binding heterocyclic compound binding pyrimidine nucleotide 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 nucleotide binding heterocyclic compound binding pyrimidine nucleotide binding small molecule binding cation binding ion 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 ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine nucleoside 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 ribonucleotide 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 purine nucleotide catabolic process carbohydrate derivative catabolic process nucleoside monophosphate catabolic process primary metabolic process purine-containing compound catabolic process nucleotide metabolic process IMP catabolic process purine-containing compound metabolic process nucleobase-containing compound catabolic process organophosphate metabolic process metabolic process cellular process purine ribonucleotide metabolic process pyrimidine deoxyribonucleotide catabolic process pyrimidine deoxyribonucleoside monophosphate catabolic process deoxyribonucleoside monophosphate catabolic process deoxyribonucleotide catabolic process pyrimidine deoxyribonucleotide metabolic process pyrimidine-containing compound 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 pyrimidine nucleoside monophosphate catabolic process pyrimidine nucleoside monophosphate metabolic process pyrimidine-containing compound metabolic process 2'-deoxyribonucleotide metabolic process dUMP metabolic process dCMP catabolic process dCMP metabolic process dTMP catabolic process dTMP metabolic process allantoin metabolic process dGMP catabolic process purine deoxyribonucleoside monophosphate catabolic process purine deoxyribonucleotide catabolic process purine deoxyribonucleoside monophosphate metabolic process dGMP metabolic process purine deoxyribonucleotide metabolic process dephosphorylation pyrimidine ribonucleotide catabolic process pyrimidine ribonucleoside monophosphate catabolic process UMP metabolic process pyrimidine ribonucleotide metabolic process pyrimidine ribonucleoside monophosphate metabolic process UMP catabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytosol nucleus

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q8TCD5	colorectal cancer medulloblastoma colorectal carcinoma primitive neuroectodermal tumor Colorectal Neoplasms systemic sclerosis

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.

Prepare Data

Validate Data

Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 4YIH | pdb_00004yih