4DJN | pdb_00004djn

Crystal structure of a ribonucleotide reductase M2 B (RNRR2) from Homo sapiens at 2.20 A resolution

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)
B	d4djnb_	All alpha proteins	Ferritin-like	Ferritin-like	Ribonucleotide reductase-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4djna_	All alpha proteins	Ferritin-like	Ferritin-like	Ribonucleotide reductase-like	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)
B	SCOP2B Superfamily	Ferritin-like	8066790	3001658	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ferritin-like	8066790	3001658	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)
B	V-set	e4djnB1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: V-set	ECOD (v294.1)
A	Chalcone	e4djnA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: RIFT-related	T: FMN-binding split barrel 2	F: Chalcone	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.620.20	Mainly Alpha	Orthogonal Bundle	Ribonucleotide Reductase, subunit A	Ribonucleotide Reductase, subunit A	CATH (4.3.0)
A	1.10.620.20	Mainly Alpha	Orthogonal Bundle	Ribonucleotide Reductase, subunit A	Ribonucleotide Reductase, subunit A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00268	Ribonucleotide reductase, small chain (Ribonuc_red_sm)	Ribonucleotide reductase, small chain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Ribonucleoside-diphosphate reductase subunit M2 B	ribonucleoside-diphosphate reductase activity oxidoreductase activity oxidoreductase activity, acting on CH or CH2 groups oxidoreductase activity, acting on CH or CH2 groups, disulfide as acceptor ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor catalytic activity cation binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding	nucleoside phosphate metabolic process primary metabolic process nucleobase-containing compound metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process nucleoside triphosphate metabolic process phosphorus metabolic process deoxyribonucleoside triphosphate metabolic process positive regulation of G0 to G1 transition regulation of biological process nucleoside phosphate metabolic process primary metabolic process nucleobase-containing compound metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process nucleoside triphosphate metabolic process phosphorus metabolic process deoxyribonucleoside triphosphate metabolic process positive regulation of G0 to G1 transition regulation of biological process regulation of cellular process regulation of cell cycle process biological regulation positive regulation of biological process G0 to G1 transition positive regulation of cell cycle regulation of G0 to G1 transition positive regulation of cell cycle process cell cycle regulation of cell cycle positive regulation of cellular process cell cycle process multicellular organismal process renal system process system process cellular response to stimulus response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction regulation of programmed cell death regulation of intrinsic apoptotic signaling pathway intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction negative regulation of apoptotic signaling pathway regulation of signal transduction by p53 class mediator negative regulation of cellular process signal transduction intrinsic apoptotic signaling pathway negative regulation of signal transduction by p53 class mediator regulation of signaling negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process signal transduction by p53 class mediator cell death negative regulation of signal transduction apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway negative regulation of apoptotic process negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator regulation of response to stimulus regulation of cell communication intrinsic apoptotic signaling pathway by p53 class mediator apoptotic process regulation of intrinsic apoptotic signaling pathway by p53 class mediator programmed cell death regulation of apoptotic signaling pathway nucleoside diphosphate metabolic process ribonucleoside diphosphate metabolic process DNA-templated DNA replication DNA metabolic process nucleic acid metabolic process mitochondrial DNA metabolic process DNA replication mitochondrial DNA replication macromolecule metabolic process carbohydrate derivative biosynthetic process deoxyribose phosphate biosynthetic process nucleotide biosynthetic process 2'-deoxyribonucleotide metabolic process 2'-deoxyribonucleotide biosynthetic process carbohydrate derivative metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process biosynthetic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process cellular response to stress DNA damage response response to stress DNA repair response to oxidative stress DNA synthesis involved in DNA repair macromolecule biosynthetic process nucleic acid biosynthetic process DNA biosynthetic process developmental process multicellular organism development anatomical structure development animal organ development kidney development renal system development system development regulation of cell cycle phase transition G2/M transition of mitotic cell cycle cell cycle phase transition mitotic cell cycle regulation of mitotic cell cycle positive regulation of mitotic cell cycle phase transition positive regulation of mitotic cell cycle cell cycle G2/M phase transition positive regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of cell cycle G2/M phase transition positive regulation of cell cycle G2/M phase transition regulation of mitotic cell cycle phase transition mitotic cell cycle process positive regulation of cell cycle phase transition mitotic cell cycle phase transition response to amine response to chemical response to nitrogen compound deoxyribonucleotide biosynthetic process deoxyribonucleotide metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex oxidoreductase complex cytosol ribonucleoside-diphosphate reductase complex nucleus membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex oxidoreductase complex cytosol ribonucleoside-diphosphate reductase complex nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR012348	Ribonucleotide reductase-like	Homologous Superfamily
A, B	IPR000358	Ribonucleotide reductase small subunit family	Family
A, B	IPR030475	Ribonucleotide reductase small subunit, acitve site	Active Site
A, B	IPR033909	Ribonucleotide reductase small subunit	Family
A, B	IPR009078	Ferritin-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q7LG56	mitochondrial DNA depletion syndrome 8a progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 5 progressive external ophthalmoplegia Kearns-Sayre syndrome inborn mitochondrial myopathy myopathy peripheral neuropathy progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1 Muscle Hypotonia kidney disease mitochondrial DNA depletion syndrome 1 muscle tissue disease acquired lactic acidosis peripheral nervous system disease atypical teratoid rhabdoid tumor mitochondrial DNA depletion syndrome 8a progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 5 progressive external ophthalmoplegia Kearns-Sayre syndrome inborn mitochondrial myopathy myopathy peripheral neuropathy progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1 Muscle Hypotonia kidney disease mitochondrial DNA depletion syndrome 1 muscle tissue disease acquired lactic acidosis peripheral nervous system disease atypical teratoid rhabdoid tumor rhabdomyolysis intellectual disability lactic acidosis mitochondrial neurogastrointestinal encephalomyopathy adult-onset chronic progressive external ophthalmoplegia with mitochondrial myopathy congenital anomaly of kidney and urinary tract subependymal giant cell astrocytoma large cell medulloblastoma medulloblastoma mitochondrial DNA depletion syndrome muscular disease ovarian cancer arthrogryposis tuberculosis leukodystrophy

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.