7MDI

Structure of the Neisseria gonorrhoeae ribonucleotide reductase in the inactive state

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)
B [auth E]	SCOP2B Superfamily	Ferritin-like	8106304	3001658	SCOP2B (2022-06-29)
D [auth G]	SCOP2B Superfamily	Ferritin-like	8106304	3001658	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ferritin-like	8106304	3001658	SCOP2B (2022-06-29)
H	SCOP2 Family	Ribonucleotide reductase-like	8106303	4000846	SCOP2 (2022-06-29)
H	SCOP2 Superfamily	Ferritin-like	8106304	3001658	SCOP2 (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	PF03477	e7mdiA3	A: alpha arrays	X: RuvA-C	H: ATP cone (From Topology)	T: ATP cone	F: PF03477	ECOD (1.6)
A	PF00317	e7mdiA2	A: alpha arrays	X: Alpha helical domain of ribonucleotide reductases (From Topology)	H: Alpha helical domain of ribonucleotide reductases (From Topology)	T: Alpha helical domain of ribonucleotide reductases	F: PF00317	ECOD (1.6)
A	PF02867	e7mdiA1	A: a/b barrels	X: Ten stranded beta/alpha barrel (From Topology)	H: Ten stranded beta/alpha barrel (From Topology)	T: Ten stranded beta/alpha barrel	F: PF02867	ECOD (1.6)
C [auth B]	PF03477	e7mdiB3	A: alpha arrays	X: RuvA-C	H: ATP cone (From Topology)	T: ATP cone	F: PF03477	ECOD (1.6)
C [auth B]	PF00317	e7mdiB2	A: alpha arrays	X: Alpha helical domain of ribonucleotide reductases (From Topology)	H: Alpha helical domain of ribonucleotide reductases (From Topology)	T: Alpha helical domain of ribonucleotide reductases	F: PF00317	ECOD (1.6)
C [auth B]	PF02867	e7mdiB1	A: a/b barrels	X: Ten stranded beta/alpha barrel (From Topology)	H: Ten stranded beta/alpha barrel (From Topology)	T: Ten stranded beta/alpha barrel	F: PF02867	ECOD (1.6)
E [auth D]	PF03477	e7mdiD3	A: alpha arrays	X: RuvA-C	H: ATP cone (From Topology)	T: ATP cone	F: PF03477	ECOD (1.6)
E [auth D]	PF00317	e7mdiD2	A: alpha arrays	X: Alpha helical domain of ribonucleotide reductases (From Topology)	H: Alpha helical domain of ribonucleotide reductases (From Topology)	T: Alpha helical domain of ribonucleotide reductases	F: PF00317	ECOD (1.6)
E [auth D]	PF02867	e7mdiD1	A: a/b barrels	X: Ten stranded beta/alpha barrel (From Topology)	H: Ten stranded beta/alpha barrel (From Topology)	T: Ten stranded beta/alpha barrel	F: PF02867	ECOD (1.6)
G [auth C]	PF03477	e7mdiC3	A: alpha arrays	X: RuvA-C	H: ATP cone (From Topology)	T: ATP cone	F: PF03477	ECOD (1.6)
G [auth C]	PF00317	e7mdiC2	A: alpha arrays	X: Alpha helical domain of ribonucleotide reductases (From Topology)	H: Alpha helical domain of ribonucleotide reductases (From Topology)	T: Alpha helical domain of ribonucleotide reductases	F: PF00317	ECOD (1.6)
G [auth C]	PF02867	e7mdiC1	A: a/b barrels	X: Ten stranded beta/alpha barrel (From Topology)	H: Ten stranded beta/alpha barrel (From Topology)	T: Ten stranded beta/alpha barrel	F: PF02867	ECOD (1.6)
B [auth E]	PF00268	e7mdiE1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: PF00268	ECOD (1.6)
D [auth G]	PF00268	e7mdiG1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: PF00268	ECOD (1.6)
F	PF00268	e7mdiF1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: PF00268	ECOD (1.6)
H	PF00268	e7mdiH1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: PF00268	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B], E [auth D], G [auth C]	PF02867	Ribonucleotide reductase, barrel domain (Ribonuc_red_lgC)	Ribonucleotide reductase, barrel domain	-	Family
A, C [auth B], E [auth D], G [auth C]	PF00317	Ribonucleotide reductase, all-alpha domain (Ribonuc_red_lgN)	Ribonucleotide reductase, all-alpha domain	-	Domain
A, C [auth B], E [auth D], G [auth C]	PF03477	ATP cone domain (ATP-cone)	ATP cone domain	-	Domain
B [auth E], D [auth G], F, H	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, C [auth B], E [auth D], G [auth C]	Ribonucleoside-diphosphate reductase subunit alpha	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide 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	nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process nucleotide biosynthetic process carbohydrate derivative metabolic process deoxyribonucleotide biosynthetic process deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process nucleotide biosynthetic process carbohydrate derivative metabolic process deoxyribonucleotide biosynthetic process deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process organic substance biosynthetic process small molecule metabolic process phosphorus metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process cellular metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process organic cyclic compound biosynthetic process nucleoside phosphate biosynthetic process cellular process	protein-containing complex intracellular anatomical structure catalytic complex oxidoreductase complex cytoplasm cellular anatomical entity cytosol ribonucleoside-diphosphate reductase complex
B [auth E], D [auth G], F, H	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	nucleotide biosynthetic process carbohydrate derivative metabolic process nucleobase-containing compound metabolic process deoxyribonucleotide biosynthetic process organic substance metabolic process deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process organic substance biosynthetic process small molecule metabolic process phosphorus metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process cellular metabolic process nucleotide biosynthetic process carbohydrate derivative metabolic process nucleobase-containing compound metabolic process deoxyribonucleotide biosynthetic process organic substance metabolic process deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process organic substance biosynthetic process small molecule metabolic process phosphorus metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process cellular metabolic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process organic cyclic compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process organic cyclic compound biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B], E [auth D], G [auth C]	IPR008926	Ribonucleotide reductase R1 subunit, N-terminal	Homologous Superfamily
A, C [auth B], E [auth D], G [auth C]	IPR013509	Ribonucleotide reductase large subunit, N-terminal	Domain
A, C [auth B], E [auth D], G [auth C]	IPR013346	Ribonucleotide reductase, class I, alpha subunit, C-terminal	Domain
A, C [auth B], E [auth D], G [auth C]	IPR000788	Ribonucleotide reductase large subunit, C-terminal	Domain
A, C [auth B], E [auth D], G [auth C]	IPR039718	Ribonucleoside-diphosphate reductase large subunit	Family
A, C [auth B], E [auth D], G [auth C]	IPR005144	ATP-cone domain	Domain
B [auth E], D [auth G], F, H	IPR009078	Ferritin-like superfamily	Homologous Superfamily
B [auth E], D [auth G], F, H	IPR000358	Ribonucleotide reductase small subunit family	Family
B [auth E], D [auth G], F, H	IPR030475	Ribonucleotide reductase small subunit, acitve site	Active Site
B [auth E], D [auth G], F, H	IPR033909	Ribonucleotide reductase small subunit	Family
B [auth E], D [auth G], F, H	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 R01GM133198.