4E4E | pdb_00004e4e

Crystal Structure of the Y34F mutant of Saccharomyces cerevisiae Manganese Superoxide Dismutase

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
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d4e4ed1	All alpha proteins	Long alpha-hairpin	Fe,Mn superoxide dismutase (SOD), N-terminal domain	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d4e4ed2	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	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d4e4ec1	All alpha proteins	Long alpha-hairpin	Fe,Mn superoxide dismutase (SOD), N-terminal domain	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d4e4ec2	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	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d4e4eb1	All alpha proteins	Long alpha-hairpin	Fe,Mn superoxide dismutase (SOD), N-terminal domain	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d4e4eb2	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	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d4e4ea1	All alpha proteins	Long alpha-hairpin	Fe,Mn superoxide dismutase (SOD), N-terminal domain	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d4e4ea2	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	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Ank_2, Ank_4, Ank_5	e4e4eD3	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Ank_2, Ank_4, Ank_5	ECOD (v294.1)
C	Ank_2, Ank_4, Ank_5	e4e4eC3	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Ank_2, Ank_4, Ank_5	ECOD (v294.1)
B	Ank_2, Ank_4, Ank_5	e4e4eB3	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Ank_2, Ank_4, Ank_5	ECOD (v294.1)
A	Ank_2, Ank_4, Ank_5	e4e4eA3	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Ank_2, Ank_4, Ank_5	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 [Mn], mitochondrial	cation binding manganese ion binding transition metal ion 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	reactive oxygen species metabolic process metabolic process cellular process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen

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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D	MLY	Parent Component: LYS RESID: AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084

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.

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