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
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	Fer4_13	e3qvdH3	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Fer4_13	ECOD (develop294)
G	Fer4_13	e3qvdG3	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Fer4_13	ECOD (develop294)
F	Fer4_13	e3qvdF3	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Fer4_13	ECOD (develop294)
E	Fer4_13	e3qvdE3	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Fer4_13	ECOD (develop294)
D	Fer4_13	e3qvdD3	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Fer4_13	ECOD (develop294)
D		e3qvdD2	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F:	ECOD (develop294)
C	Fer4_13	e3qvdC3	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Fer4_13	ECOD (develop294)
B	Fer4_13	e3qvdB3	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Fer4_13	ECOD (develop294)
A	Fer4_13	e3qvdA3	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Fer4_13	ECOD (develop294)

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)

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.