3EVK | pdb_00003evk

Crystal structure of the metal-bound superoxide dismutase from Pyrobaculum aerophilum

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)
D	d3evkd1	All alpha proteins	Long alpha-hairpin	Fe,Mn superoxide dismutase (SOD), N-terminal domain	Fe,Mn superoxide dismutase (SOD), N-terminal domain	Fe superoxide dismutase (FeSOD)	(Pyrobaculum aerophilum ) [TaxId: 13773 ],	SCOPe (2.08)
D	d3evkd2	Alpha and beta proteins (a+b)	Fe,Mn superoxide dismutase (SOD), C-terminal domain	Fe,Mn superoxide dismutase (SOD), C-terminal domain	Fe,Mn superoxide dismutase (SOD), C-terminal domain	Fe superoxide dismutase (FeSOD)	(Pyrobaculum aerophilum ) [TaxId: 13773 ],	SCOPe (2.08)
D	d3evkd3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Pyrobaculum aerophilum ) [TaxId: 13773 ],	SCOPe (2.08)
C	d3evkc1	All alpha proteins	Long alpha-hairpin	Fe,Mn superoxide dismutase (SOD), N-terminal domain	Fe,Mn superoxide dismutase (SOD), N-terminal domain	Fe superoxide dismutase (FeSOD)	(Pyrobaculum aerophilum ) [TaxId: 13773 ],	SCOPe (2.08)
C	d3evkc2	Alpha and beta proteins (a+b)	Fe,Mn superoxide dismutase (SOD), C-terminal domain	Fe,Mn superoxide dismutase (SOD), C-terminal domain	Fe,Mn superoxide dismutase (SOD), C-terminal domain	Fe superoxide dismutase (FeSOD)	(Pyrobaculum aerophilum ) [TaxId: 13773 ],	SCOPe (2.08)
C	d3evkc3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Pyrobaculum aerophilum ) [TaxId: 13773 ],	SCOPe (2.08)
B	d3evkb1	All alpha proteins	Long alpha-hairpin	Fe,Mn superoxide dismutase (SOD), N-terminal domain	Fe,Mn superoxide dismutase (SOD), N-terminal domain	Fe superoxide dismutase (FeSOD)	(Pyrobaculum aerophilum ) [TaxId: 13773 ],	SCOPe (2.08)
B	d3evkb2	Alpha and beta proteins (a+b)	Fe,Mn superoxide dismutase (SOD), C-terminal domain	Fe,Mn superoxide dismutase (SOD), C-terminal domain	Fe,Mn superoxide dismutase (SOD), C-terminal domain	Fe superoxide dismutase (FeSOD)	(Pyrobaculum aerophilum ) [TaxId: 13773 ],	SCOPe (2.08)
B	d3evkb3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Pyrobaculum aerophilum ) [TaxId: 13773 ],	SCOPe (2.08)
A	d3evka1	All alpha proteins	Long alpha-hairpin	Fe,Mn superoxide dismutase (SOD), N-terminal domain	Fe,Mn superoxide dismutase (SOD), N-terminal domain	Fe superoxide dismutase (FeSOD)	(Pyrobaculum aerophilum ) [TaxId: 13773 ],	SCOPe (2.08)
A	d3evka2	Alpha and beta proteins (a+b)	Fe,Mn superoxide dismutase (SOD), C-terminal domain	Fe,Mn superoxide dismutase (SOD), C-terminal domain	Fe,Mn superoxide dismutase (SOD), C-terminal domain	Fe superoxide dismutase (FeSOD)	(Pyrobaculum aerophilum ) [TaxId: 13773 ],	SCOPe (2.08)
A	d3evka3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Pyrobaculum aerophilum ) [TaxId: 13773 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Fe, Mn superoxide dismutase (SOD), N-terminal domain	8038311	3000794	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Fe, Mn superoxide dismutase (SOD), C-terminal domain	8038313	3000916	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Fe, Mn superoxide dismutase (SOD), C-terminal domain	8038313	3000916	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Fe, Mn superoxide dismutase (SOD), N-terminal domain	8038311	3000794	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Fe, Mn superoxide dismutase (SOD), N-terminal domain	8038311	3000794	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Fe, Mn superoxide dismutase (SOD), C-terminal domain	8038313	3000916	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Fe, Mn superoxide dismutase (SOD), C-terminal domain	8038313	3000916	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Fe, Mn superoxide dismutase (SOD), N-terminal domain	8038311	3000794	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)
D	MTHFR	e3evkD1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: MTHFR	ECOD (v294.1)
C	MTHFR	e3evkC1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: MTHFR	ECOD (v294.1)
B	MTHFR	e3evkB1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: MTHFR	ECOD (v294.1)
A	Fz	e3evkA1	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: SH3	T: SH3	F: Fz	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.10.287.990	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Fe,Mn superoxide dismutase (SOD) domain	CATH (4.3.0)
D	3.55.40.20	Alpha Beta	3-Layer(bab) Sandwich	minor pseudopilin epsh fold	Iron/manganese superoxide dismutase, C-terminal domain	CATH (4.3.0)
C	1.10.287.990	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Fe,Mn superoxide dismutase (SOD) domain	CATH (4.3.0)
C	3.55.40.20	Alpha Beta	3-Layer(bab) Sandwich	minor pseudopilin epsh fold	Iron/manganese superoxide dismutase, C-terminal domain	CATH (4.3.0)
B	1.10.287.990	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Fe,Mn superoxide dismutase (SOD) domain	CATH (4.3.0)
B	3.55.40.20	Alpha Beta	3-Layer(bab) Sandwich	minor pseudopilin epsh fold	Iron/manganese superoxide dismutase, C-terminal domain	CATH (4.3.0)
A	1.10.287.990	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Fe,Mn superoxide dismutase (SOD) domain	CATH (4.3.0)
A	3.55.40.20	Alpha Beta	3-Layer(bab) Sandwich	minor pseudopilin epsh fold	Iron/manganese superoxide dismutase, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00081	Iron/manganese superoxide dismutases, alpha-hairpin domain (Sod_Fe_N)	Iron/manganese superoxide dismutases, alpha-hairpin domain	superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplas ...	superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplasmic Cu/Zn SOD, and a mitochondrial Mn/Fe SOD. N-terminal domain is a long alpha antiparallel hairpin. A small fragment of YTRE_LEPBI matches well - sequencing error?	Domain
A, B, C, D	PF02777	Iron/manganese superoxide dismutases, C-terminal domain (Sod_Fe_C)	Iron/manganese superoxide dismutases, C-terminal domain	superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplas ...	superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplasmic Cu/Zn SOD, and a mitochondrial Mn/Fe SOD. C-terminal domain is a mixed alpha/beta fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Superoxide dismutase [Fe]	cation binding ion binding binding metal ion binding small molecule binding superoxide dismutase activity oxidoreductase activity, acting on superoxide radicals as acceptor oxidoreductase activity antioxidant activity catalytic activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036324	Manganese/iron superoxide dismutase, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR001189	Manganese/iron superoxide dismutase	Family
A, B, C, D	IPR050265	Iron/Manganese Superoxide Dismutase	Family
A, B, C, D	IPR019833	Manganese/iron superoxide dismutase, binding site	Binding Site
A, B, C, D	IPR019832	Manganese/iron superoxide dismutase, C-terminal	Domain
A, B, C, D	IPR019831	Manganese/iron superoxide dismutase, N-terminal	Domain
A, B, C, D	IPR036314	Manganese/iron superoxide dismutase, C-terminal domain superfamily	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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.