7Z3D | pdb_00007z3d

XFEL structure of Class Ib ribonucleotide reductase dimanganese(II) NrdF in complex with oxidized NrdI from Bacillus cereus

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ferritin-like	8066784	3001658	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Flavoproteins	8081775	3001217	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	Ribonuc_red_sm	e7z3dA1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: Ribonuc_red_sm	ECOD (1.6)
B	Flavodoxin_NdrI	e7z3dB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: Flavoproteins	F: Flavodoxin_NdrI	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00268	Ribonucleotide reductase, small chain (Ribonuc_red_sm)	Ribonucleotide reductase, small chain		Domain
B	PF07972	NrdI Flavodoxin like (Flavodoxin_NdrI)	NrdI Flavodoxin like		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ribonucleoside-diphosphate reductase subunit beta	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	nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process nucleobase-containing compound metabolic process deoxyribonucleotide biosynthetic process deoxyribonucleotide metabolic process biosynthetic process organophosphate metabolic process nucleobase-containing small molecule metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process nucleobase-containing compound metabolic process deoxyribonucleotide biosynthetic process deoxyribonucleotide metabolic process biosynthetic process organophosphate metabolic process nucleobase-containing small molecule metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process nucleoside phosphate biosynthetic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process	cellular anatomical structure membrane protein-containing complex intracellular anatomical structure catalytic complex oxidoreductase complex cytoplasm cytosol ribonucleoside-diphosphate reductase complex
B	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	macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process	-

InterPro: Protein Family Classification InterPro Database Homepage

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

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.