1I08 | pdb_00001i08

CRYSTAL STRUCTURE ANALYSIS OF THE H30A MUTANT OF MANGANESE SUPEROXIDE DISMUTASE FROM E. COLI

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	d1i08d1	All alpha proteins	Long alpha-hairpin	Fe,Mn superoxide dismutase (SOD), N-terminal domain	Fe,Mn superoxide dismutase (SOD), N-terminal domain	Mn superoxide dismutase (MnSOD)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1i08d2	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	Mn superoxide dismutase (MnSOD)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1i08c1	All alpha proteins	Long alpha-hairpin	Fe,Mn superoxide dismutase (SOD), N-terminal domain	Fe,Mn superoxide dismutase (SOD), N-terminal domain	Mn superoxide dismutase (MnSOD)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1i08c2	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	Mn superoxide dismutase (MnSOD)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1i08b1	All alpha proteins	Long alpha-hairpin	Fe,Mn superoxide dismutase (SOD), N-terminal domain	Fe,Mn superoxide dismutase (SOD), N-terminal domain	Mn superoxide dismutase (MnSOD)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1i08b2	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	Mn superoxide dismutase (MnSOD)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1i08a1	All alpha proteins	Long alpha-hairpin	Fe,Mn superoxide dismutase (SOD), N-terminal domain	Fe,Mn superoxide dismutase (SOD), N-terminal domain	Mn superoxide dismutase (MnSOD)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1i08a2	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	Mn superoxide dismutase (MnSOD)	(Escherichia coli ) [TaxId: 562 ],	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), C-terminal domain	8042546	3000916	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Fe, Mn superoxide dismutase (SOD), N-terminal domain	8042545	3000794	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Fe, Mn superoxide dismutase (SOD), C-terminal domain	8042546	3000916	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Fe, Mn superoxide dismutase (SOD), N-terminal domain	8042545	3000794	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Fe, Mn superoxide dismutase (SOD), C-terminal domain	8042546	3000916	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Fe, Mn superoxide dismutase (SOD), N-terminal domain	8042545	3000794	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Fe, Mn superoxide dismutase (SOD), C-terminal domain	8042546	3000916	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Fe, Mn superoxide dismutase (SOD), N-terminal domain	8042545	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	Seryl_tRNA_N	e1i08D1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: tRNA-binding arm	T: tRNA-binding arm	F: Seryl_tRNA_N	ECOD (v294.1)
D	NTP_transf_2, PAP_NTPase	e1i08D2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: NTP_transf_2, PAP_NTPase	ECOD (v294.1)
C	Seryl_tRNA_N	e1i08C1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: tRNA-binding arm	T: tRNA-binding arm	F: Seryl_tRNA_N	ECOD (v294.1)
C	NTP_transf_2, PAP_NTPase	e1i08C2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: NTP_transf_2, PAP_NTPase	ECOD (v294.1)
B	Seryl_tRNA_N	e1i08B1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: tRNA-binding arm	T: tRNA-binding arm	F: Seryl_tRNA_N	ECOD (v294.1)
B	NTP_transf_2, PAP_NTPase	e1i08B2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: NTP_transf_2, PAP_NTPase	ECOD (v294.1)
A	Seryl_tRNA_N	e1i08A1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: tRNA-binding arm	T: tRNA-binding arm	F: Seryl_tRNA_N	ECOD (v294.1)
A	NTP_transf_2, PAP_NTPase	e1i08A2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: NTP_transf_2, PAP_NTPase	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	MANGANESE SUPEROXIDE DISMUTASE	DNA binding binding nucleic acid binding identical protein binding protein binding protein homodimerization activity protein dimerization activity antioxidant activity superoxide dismutase activity oxidoreductase activity, acting on superoxide radicals as acceptor oxidoreductase activity catalytic activity cation binding manganese ion binding DNA binding binding nucleic acid binding identical protein binding protein binding protein homodimerization activity protein dimerization activity antioxidant activity superoxide dismutase activity oxidoreductase activity, acting on superoxide radicals as acceptor oxidoreductase 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 response to pH response to abiotic stimulus response to acidic pH response to heat response to temperature stimulus cellular response to metal ion cellular response to selenium ion response to metal ion response to selenium ion	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

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	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.