3QVD | pdb_00003qvd

Exposure of rubrerythrin from Pyrococcus furiosus to peroxide, fifteen second time point.

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)
H	d3qvdh1	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	automated matches	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
H	d3qvdh2	Small proteins	Rubredoxin-like	Rubredoxin-like	automated matches	automated matches	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
G	d3qvdg1	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	automated matches	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
G	d3qvdg2	Small proteins	Rubredoxin-like	Rubredoxin-like	automated matches	automated matches	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
F	d3qvdf1	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	automated matches	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
F	d3qvdf2	Small proteins	Rubredoxin-like	Rubredoxin-like	automated matches	automated matches	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
E	d3qvde1	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	automated matches	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
E	d3qvde2	Small proteins	Rubredoxin-like	Rubredoxin-like	automated matches	automated matches	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
D	d3qvdd1	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	automated matches	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
D	d3qvdd2	Small proteins	Rubredoxin-like	Rubredoxin-like	automated matches	automated matches	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
C	d3qvdc1	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	automated matches	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
C	d3qvdc2	Small proteins	Rubredoxin-like	Rubredoxin-like	automated matches	automated matches	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
B	d3qvdb1	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	automated matches	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
B	d3qvdb2	Small proteins	Rubredoxin-like	Rubredoxin-like	automated matches	automated matches	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
A	d3qvda1	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	automated matches	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
A	d3qvda2	Small proteins	Rubredoxin-like	Rubredoxin-like	automated matches	automated matches	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Rubredoxin-like	8036856	3001257	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ferritin-like	8036854	3001658	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Rubredoxin-like	8036856	3001257	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ferritin-like	8036854	3001658	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Rubredoxin-like	8036856	3001257	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ferritin-like	8036854	3001658	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ferritin-like	8036854	3001658	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Rubredoxin-like	8036856	3001257	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ferritin-like	8036854	3001658	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Rubredoxin-like	8036856	3001257	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Rubredoxin-like	8036856	3001257	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ferritin-like	8036854	3001658	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ferritin-like	8036854	3001658	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Rubredoxin-like	8036856	3001257	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Rubredoxin-like	8036856	3001257	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ferritin-like	8036854	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)
H	Rubrerythrin	e3qvdH3	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Ferritin/Heme oxygenase	T: Ferritin	F: Rubrerythrin	ECOD (1.6)
H	Rubredoxin_1	e3qvdH4	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Rubredoxin_1	ECOD (1.6)
G	Rubrerythrin	e3qvdG3	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Ferritin/Heme oxygenase	T: Ferritin	F: Rubrerythrin	ECOD (1.6)
G	Rubredoxin_1	e3qvdG4	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Rubredoxin_1	ECOD (1.6)
F	Rubrerythrin	e3qvdF3	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Ferritin/Heme oxygenase	T: Ferritin	F: Rubrerythrin	ECOD (1.6)
F	Rubredoxin_1	e3qvdF4	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Rubredoxin_1	ECOD (1.6)
E	Rubrerythrin	e3qvdE3	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Ferritin/Heme oxygenase	T: Ferritin	F: Rubrerythrin	ECOD (1.6)
E	Rubredoxin_1	e3qvdE4	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Rubredoxin_1	ECOD (1.6)
D	Rubrerythrin	e3qvdD3	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Ferritin/Heme oxygenase	T: Ferritin	F: Rubrerythrin	ECOD (1.6)
D	Rubredoxin_1	e3qvdD2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Rubredoxin_1	ECOD (1.6)
C	Rubrerythrin	e3qvdC3	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Ferritin/Heme oxygenase	T: Ferritin	F: Rubrerythrin	ECOD (1.6)
C	Rubredoxin_1	e3qvdC4	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Rubredoxin_1	ECOD (1.6)
B	Rubrerythrin	e3qvdB3	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Ferritin/Heme oxygenase	T: Ferritin	F: Rubrerythrin	ECOD (1.6)
B	Rubredoxin_1	e3qvdB4	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Rubredoxin_1	ECOD (1.6)
A	Rubrerythrin	e3qvdA3	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Ferritin/Heme oxygenase	T: Ferritin	F: Rubrerythrin	ECOD (1.6)
A	Rubredoxin_1	e3qvdA4	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Rubredoxin_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
H	2.20.28.10	Mainly Beta	Single Sheet	Rubrerythrin, domain 2		CATH (4.3.0)
G	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
G	2.20.28.10	Mainly Beta	Single Sheet	Rubrerythrin, domain 2		CATH (4.3.0)
F	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
F	2.20.28.10	Mainly Beta	Single Sheet	Rubrerythrin, domain 2		CATH (4.3.0)
E	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
E	2.20.28.10	Mainly Beta	Single Sheet	Rubrerythrin, domain 2		CATH (4.3.0)
D	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
D	2.20.28.10	Mainly Beta	Single Sheet	Rubrerythrin, domain 2		CATH (4.3.0)
C	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
C	2.20.28.10	Mainly Beta	Single Sheet	Rubrerythrin, domain 2		CATH (4.3.0)
B	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
B	2.20.28.10	Mainly Beta	Single Sheet	Rubrerythrin, domain 2		CATH (4.3.0)
A	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
A	2.20.28.10	Mainly Beta	Single Sheet	Rubrerythrin, domain 2		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF02915	Rubrerythrin (Rubrerythrin)	Rubrerythrin	This domain has a ferritin-like fold.	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	PF21349	Rubrerythrin, rubredoxin-like domain (RUBY_RBDX)	Rubrerythrin, rubredoxin-like domain	Rubrerythrin (RUBY) is a fusion protein containing an N-terminal diiron-binding domain (Pfam:PF02915) and a C-terminal rubredoxin-like domain. RUBY may play a role in oxidative stress. This entry represents the rubredoxin-like domain of RUBY and rev ...	Rubrerythrin (RUBY) is a fusion protein containing an N-terminal diiron-binding domain (Pfam:PF02915) and a C-terminal rubredoxin-like domain. RUBY may play a role in oxidative stress. This entry represents the rubredoxin-like domain of RUBY and reverse rubrerythrin 1/2 from Clostridium acetobutylicum (RRBR1/2) [1-5]. RRBRs function as the terminal component of an NADH peroxidase when using NADH:rubredoxin oxidoreductase (NROR) as the electron transport intermediary from NADH to RRBRs and play an important role in the oxidative stress defense system of C. acetobutylicum [6].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Rubrerythrin	oxidoreductase activity catalytic activity cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR009040	Ferritin-like diiron domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR012347	Ferritin-like	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR009078	Ferritin-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR024934	Rubredoxin-like domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR003251	Rubrerythrin, diiron-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR052753	Rubrerythrin-2/Nigerythrin	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR048574	Rubrerythrin, rubredoxin-like domain	Domain

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.