3N39 | pdb_00003n39

Ribonucleotide Reductase Dimanganese(II)-NrdF from Escherichia coli in Complex with NrdI

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C [auth A]	d3n39a_	All alpha proteins	Ferritin-like	Ferritin-like	Ribonucleotide reductase-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A [auth B]	d3n39b_	All alpha proteins	Ferritin-like	Ferritin-like	Ribonucleotide reductase-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Flavoproteins	8081781	3001217	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Flavoproteins	8081781	3001217	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Ferritin-like	8066776	3001658	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	Ferritin-like	8066776	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)
D	F5_F8_type_C	e3n39D1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: F5_F8_type_C	ECOD (v294.1)
B [auth C]	RRM_1	e3n39C1	A: a/b three-layered sandwiches	X: Retrovirus capsid protein	H: Ubiquitin-related	T: Ubiquitin-like	F: RRM_1	ECOD (v294.1)
C [auth A]	F5_F8_type_C	e3n39A1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: F5_F8_type_C	ECOD (v294.1)
A [auth B]	F5_F8_type_C	e3n39B1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: F5_F8_type_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
B [auth C]	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
C [auth A]	1.10.620.20	Mainly Alpha	Orthogonal Bundle	Ribonucleotide Reductase, subunit A	Ribonucleotide Reductase, subunit A	CATH (4.3.0)
A [auth B]	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
B [auth C], D	PF07972	NrdI Flavodoxin like (Flavodoxin_NdrI)	NrdI Flavodoxin like		Domain
A [auth B], C [auth A]	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
B [auth C], D	Protein nrdI	FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding	-	-
A [auth B], C [auth A]	Ribonucleoside-diphosphate reductase 2 subunit beta	cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding 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	nucleoside phosphate metabolic process primary metabolic process nucleobase-containing compound metabolic process nucleoside diphosphate metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process ribonucleoside diphosphate metabolic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process carbohydrate derivative biosynthetic process deoxyribose phosphate biosynthetic process nucleoside phosphate metabolic process primary metabolic process nucleobase-containing compound metabolic process nucleoside diphosphate metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process ribonucleoside diphosphate metabolic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus 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 deoxyribonucleotide biosynthetic process deoxyribonucleotide metabolic process	protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex oxidoreductase complex cytoplasm cytosol ribonucleoside-diphosphate reductase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C], D	IPR029039	Flavoprotein-like superfamily	Homologous Superfamily
B [auth C], D	IPR004465	Ribonucleotide reductase Class Ib, NrdI	Family
B [auth C], D	IPR020852	Ribonucleotide reductase, class Ib, NrdI, bacterial	Family
A [auth B], C [auth A]	IPR009078	Ferritin-like superfamily	Homologous Superfamily
A [auth B], C [auth A]	IPR026494	Ribonucleoside-diphosphate reductase subunit beta	Family
A [auth B], C [auth A]	IPR000358	Ribonucleotide reductase small subunit family	Family
A [auth B], C [auth A]	IPR030475	Ribonucleotide reductase small subunit, acitve site	Active Site
A [auth B], C [auth A]	IPR033909	Ribonucleotide reductase small subunit	Family
A [auth B], C [auth A]	IPR012348	Ribonucleotide reductase-like	Homologous Superfamily

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.