4ERP

Crystal structure of a gemcitabine-diphosphate inhibited E. coli class Ia ribonucleotide reductase complex

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	PFL-like glycyl radical enzymes	8043875	3001069	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	R1 subunit of ribonucleotide reductase N-terminal domain	8038325	3000927	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	R1 subunit of ribonucleotide reductase N-terminal domain	8038325	3000927	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8043875	3001069	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	R1 subunit of ribonucleotide reductase N-terminal domain	8038325	3000927	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8043875	3001069	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	R1 subunit of ribonucleotide reductase N-terminal domain	8038325	3000927	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8043875	3001069	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ferritin-like	8032952	3001658	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ferritin-like	8032952	3001658	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ferritin-like	8032952	3001658	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ferritin-like	8032952	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)
A	ATP-cone_1	e4erpA1	A: alpha arrays	X: RuvA-C	H: ATP cone (From Topology)	T: ATP cone	F: ATP-cone_1	ECOD (1.6)
A	Ribonuc_red_lgN	e4erpA3	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: Ribonuc_red_lgN	ECOD (1.6)
A	Ribonuc_red_lgC	e4erpA2	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: Ribonuc_red_lgC	ECOD (1.6)
B	ATP-cone_1	e4erpB3	A: alpha arrays	X: RuvA-C	H: ATP cone (From Topology)	T: ATP cone	F: ATP-cone_1	ECOD (1.6)
B	Ribonuc_red_lgN	e4erpB1	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: Ribonuc_red_lgN	ECOD (1.6)
B	Ribonuc_red_lgC	e4erpB2	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: Ribonuc_red_lgC	ECOD (1.6)
C	ATP-cone_1	e4erpC1	A: alpha arrays	X: RuvA-C	H: ATP cone (From Topology)	T: ATP cone	F: ATP-cone_1	ECOD (1.6)
C	Ribonuc_red_lgN	e4erpC3	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: Ribonuc_red_lgN	ECOD (1.6)
C	Ribonuc_red_lgC	e4erpC2	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: Ribonuc_red_lgC	ECOD (1.6)
D	ATP-cone_1	e4erpD3	A: alpha arrays	X: RuvA-C	H: ATP cone (From Topology)	T: ATP cone	F: ATP-cone_1	ECOD (1.6)
D	Ribonuc_red_lgN	e4erpD4	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: Ribonuc_red_lgN	ECOD (1.6)
D	Ribonuc_red_lgC	e4erpD2	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: Ribonuc_red_lgC	ECOD (1.6)
E	Ribonuc_red_sm	e4erpE1	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)
F	Ribonuc_red_sm	e4erpF1	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)
G	Ribonuc_red_sm	e4erpG1	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)
H	Ribonuc_red_sm	e4erpH1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02867	Ribonucleotide reductase, barrel domain (Ribonuc_red_lgC)	Ribonucleotide reductase, barrel domain	-	Family
A, B, C, D	PF00317	Ribonucleotide reductase, all-alpha domain (Ribonuc_red_lgN)	Ribonucleotide reductase, all-alpha domain	-	Domain
A, B, C, D	PF03477	ATP cone domain (ATP-cone)	ATP cone domain	-	Domain
E, F, G, 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, B, C, D	Ribonucleoside-diphosphate reductase 1 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 protein folding chaperone identical protein binding protein binding	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 nucleobase-containing small molecule metabolic process small molecule metabolic process nucleobase-containing small molecule interconversion nucleoside phosphate metabolic process cellular 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 nucleobase-containing small molecule metabolic process small molecule metabolic process nucleobase-containing small molecule interconversion nucleoside phosphate metabolic process cellular metabolic process nucleoside diphosphate metabolic process organophosphate metabolic process ribonucleoside diphosphate metabolic process phosphate-containing compound metabolic process cellular process phosphorus metabolic process deoxyribose phosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process deoxyribonucleotide biosynthetic process deoxyribonucleotide metabolic process organic substance biosynthetic process carbohydrate derivative biosynthetic process 2'-deoxyribonucleotide metabolic process 2'-deoxyribonucleotide biosynthetic process nucleotide metabolic process deoxyribose phosphate metabolic process nucleobase-containing compound biosynthetic process biosynthetic process organophosphate biosynthetic process organic cyclic compound biosynthetic process nucleoside phosphate biosynthetic process	protein-containing complex intracellular anatomical structure catalytic complex oxidoreductase complex cytoplasm cellular anatomical entity cytosol ribonucleoside-diphosphate reductase complex
E, F, G, H	Ribonucleoside-diphosphate reductase 1 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 transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding identical protein 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 cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding	nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process nucleobase-containing small molecule metabolic process small molecule metabolic process metabolic process primary metabolic process nucleobase-containing small molecule interconversion nucleoside phosphate metabolic process cellular metabolic process nucleoside diphosphate metabolic process organophosphate metabolic process ribonucleoside diphosphate metabolic process phosphate-containing compound metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process nucleobase-containing small molecule metabolic process small molecule metabolic process metabolic process primary metabolic process nucleobase-containing small molecule interconversion nucleoside phosphate metabolic process cellular metabolic process nucleoside diphosphate metabolic process organophosphate metabolic process ribonucleoside diphosphate metabolic process phosphate-containing compound metabolic process cellular process phosphorus metabolic process deoxyribose phosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process deoxyribonucleotide biosynthetic process deoxyribonucleotide metabolic process organic substance biosynthetic process carbohydrate derivative biosynthetic process 2'-deoxyribonucleotide metabolic process 2'-deoxyribonucleotide biosynthetic process nucleotide metabolic process deoxyribose phosphate metabolic process nucleobase-containing compound biosynthetic process biosynthetic process organophosphate biosynthetic process organic cyclic compound biosynthetic process nucleoside phosphate biosynthetic process	protein-containing complex intracellular anatomical structure catalytic complex oxidoreductase complex cytoplasm cellular anatomical entity cytosol ribonucleoside-diphosphate reductase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR013509	Ribonucleotide reductase large subunit, N-terminal	Domain
A, B, C, D	IPR005144	ATP-cone domain	Domain
A, B, C, D	IPR008926	Ribonucleotide reductase R1 subunit, N-terminal	Homologous Superfamily
A, B, C, D	IPR013346	Ribonucleotide reductase, class I, alpha subunit, C-terminal	Domain
A, B, C, D	IPR000788	Ribonucleotide reductase large subunit, C-terminal	Domain
A, B, C, D	IPR039718	Ribonucleoside-diphosphate reductase large subunit	Family
E, F, G, H	IPR033909	Ribonucleotide reductase small subunit	Family
E, F, G, H	IPR012348	Ribonucleotide reductase-like	Homologous Superfamily
E, F, G, H	IPR009078	Ferritin-like superfamily	Homologous Superfamily
E, F, G, H	IPR000358	Ribonucleotide reductase small subunit family	Family
E, F, G, H	IPR030475	Ribonucleotide reductase small subunit, acitve site	Active Site

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.