3DC5 | pdb_00003dc5

Crystal Structure of a manganese superoxide dismutases from Caenorhabditis elegans

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
B [auth C]	d3dc5c1	All alpha proteins	Long alpha-hairpin	Fe,Mn superoxide dismutase (SOD), N-terminal domain	automated matches	automated matches	nematode (Caenorhabditis elegans ) [TaxId: 6239 ],	SCOPe (2.08)
B [auth C]	d3dc5c2	Alpha and beta proteins (a+b)	Fe,Mn superoxide dismutase (SOD), C-terminal domain	Fe,Mn superoxide dismutase (SOD), C-terminal domain	automated matches	automated matches	nematode (Caenorhabditis elegans ) [TaxId: 6239 ],	SCOPe (2.08)
B [auth C]	d3dc5c3	Artifacts	Tags	Tags	Tags	N-terminal Tags	nematode (Caenorhabditis elegans ) [TaxId: 6239 ],	SCOPe (2.08)
A	d3dc5a1	All alpha proteins	Long alpha-hairpin	Fe,Mn superoxide dismutase (SOD), N-terminal domain	automated matches	automated matches	nematode (Caenorhabditis elegans ) [TaxId: 6239 ],	SCOPe (2.08)
A	d3dc5a2	Alpha and beta proteins (a+b)	Fe,Mn superoxide dismutase (SOD), C-terminal domain	Fe,Mn superoxide dismutase (SOD), C-terminal domain	automated matches	automated matches	nematode (Caenorhabditis elegans ) [TaxId: 6239 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth C]		e3dc5C1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: BPL_C	F:	ECOD (20:10:01)
A		e3dc5A1	A: Alpha-beta plaits	X: Immunoglobulin-related	H: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	T: RRM_1	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth C]	1.10.287.990	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Fe,Mn superoxide dismutase (SOD) domain	CATH (4.3.0)
B [auth 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)
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 [auth C]	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 [auth C]	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 [auth C]	Superoxide dismutase [Mn] 2	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity superoxide dismutase activity oxidoreductase activity, acting on superoxide radicals as acceptor oxidoreductase activity antioxidant activity catalytic activity cation binding manganese ion binding transition metal ion binding ion binding identical protein binding protein binding binding protein homodimerization activity protein dimerization activity superoxide dismutase activity oxidoreductase activity, acting on superoxide radicals as acceptor oxidoreductase activity antioxidant activity catalytic activity cation binding manganese ion binding transition metal ion binding ion binding metal ion binding small molecule binding	cellular response to stimulus response to stimulus cellular response to oxidative stress detoxification reactive oxygen species metabolic process cellular response to chemical stress response to superoxide cellular oxidant detoxification cellular response to oxygen radical cellular response to reactive oxygen species cellular response to stress response to stress cellular detoxification response to oxygen-containing compound cellular response to stimulus response to stimulus cellular response to oxidative stress detoxification reactive oxygen species metabolic process cellular response to chemical stress response to superoxide cellular oxidant detoxification cellular response to oxygen radical cellular response to reactive oxygen species cellular response to stress response to stress cellular detoxification response to oxygen-containing compound cellular response to oxygen-containing compound response to reactive oxygen species response to toxic substance removal of superoxide radicals superoxide metabolic process response to oxidative stress cellular response to chemical stimulus response to chemical cellular response to superoxide metabolic process cellular process cellular response to toxic substance response to oxygen radical	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle respiratory chain complex protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C]	IPR036324	Manganese/iron superoxide dismutase, N-terminal domain superfamily	Homologous Superfamily
A, B [auth C]	IPR050265	Iron/Manganese Superoxide Dismutase	Family
A, B [auth C]	IPR001189	Manganese/iron superoxide dismutase	Family
A, B [auth C]	IPR019833	Manganese/iron superoxide dismutase, binding site	Binding Site
A, B [auth C]	IPR019832	Manganese/iron superoxide dismutase, C-terminal	Domain
A, B [auth C]	IPR019831	Manganese/iron superoxide dismutase, N-terminal	Domain
A, B [auth C]	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.