5U9M

Copper-Zinc Superoxide Dismutase is Activated through a Sulfenic Acid Intermediate at a Copper-ion Entry Site

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5u9ma_	All beta proteins	Immunoglobulin-like beta-sandwich	Cu,Zn superoxide dismutase-like	Cu,Zn superoxide dismutase-like	Cu,Zn superoxide dismutase, SOD	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5u9mc_	All beta proteins	Immunoglobulin-like beta-sandwich	Cu,Zn superoxide dismutase-like	Cu,Zn superoxide dismutase-like	Cu,Zn superoxide dismutase, SOD	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5u9mb2	All beta proteins	Immunoglobulin-like beta-sandwich	Cu,Zn superoxide dismutase-like	Cu,Zn superoxide dismutase-like	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
B	d5u9mb1	Alpha and beta proteins (a+b)	Ferredoxin-like	HMA, heavy metal-associated domain	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
D	d5u9md2	All beta proteins	Immunoglobulin-like beta-sandwich	Cu,Zn superoxide dismutase-like	Cu,Zn superoxide dismutase-like	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
D	d5u9md1	Alpha and beta proteins (a+b)	Ferredoxin-like	HMA, heavy metal-associated domain	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Cu Zn superoxide dismutase-like	8055253	3002059	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cu Zn superoxide dismutase-like	8055253	3002059	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HMA heavy metal-associated domain	8035511	3001159	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cu Zn superoxide dismutase-like	8055275	3002059	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cu Zn superoxide dismutase-like	8055275	3002059	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	HMA heavy metal-associated domain	8035511	3001159	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)
A	PF00080	e5u9mA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Cu,Zn superoxide dismutase-like	F: PF00080	ECOD (1.6)
C	PF00080	e5u9mC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Cu,Zn superoxide dismutase-like	F: PF00080	ECOD (1.6)
B	F_UNCLASSIFIED	e5u9mB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Cu,Zn superoxide dismutase-like	F: F_UNCLASSIFIED	ECOD (1.6)
B	PF00403	e5u9mB1	A: a+b two layers	X: Alpha-beta plaits	H: HMA-related	T: HMA, heavy metal-associated domain	F: PF00403	ECOD (1.6)
D	F_UNCLASSIFIED	e5u9mD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Cu,Zn superoxide dismutase-like	F: F_UNCLASSIFIED	ECOD (1.6)
D	PF00403	e5u9mD2	A: a+b two layers	X: Alpha-beta plaits	H: HMA-related	T: HMA, heavy metal-associated domain	F: PF00403	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF00080	Copper/zinc superoxide dismutase (SODC) (Sod_Cu)	Copper/zinc superoxide dismutase (SODC)	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 copper/zinc-binding family is one. Defects in the human SO ...	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 copper/zinc-binding family is one. Defects in the human SOD1 gene cause familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Structure is an eight-stranded beta sandwich, similar to the immunoglobulin fold.	Domain
B, D	PF00403	Heavy-metal-associated domain (HMA)	Heavy-metal-associated domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Superoxide dismutase [Cu-Zn]	small GTPase binding protein binding binding enzyme binding GTPase binding cation binding transition metal ion binding copper ion binding ion binding metal ion binding small molecule binding protein-folding chaperone binding identical protein binding protein phosphatase binding small GTPase binding protein binding binding enzyme binding GTPase binding cation binding transition metal ion binding copper ion binding ion binding metal ion binding small molecule binding protein-folding chaperone binding identical protein binding protein phosphatase binding phosphatase binding protein phosphatase 2B binding superoxide dismutase activity oxidoreductase activity, acting on superoxide radicals as acceptor oxidoreductase activity antioxidant activity catalytic activity zinc ion binding	intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis response to stimulus response to chemical response to xenobiotic stimulus response to stress intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis response to stimulus response to chemical response to xenobiotic stimulus response to stress response to wounding response to axon injury regulation of biological process regulation of cellular process cellular metabolic process reactive oxygen species metabolic process biological regulation positive regulation of biological process regulation of superoxide metabolic process regulation of cellular metabolic process positive regulation of cellular metabolic process positive regulation of reactive oxygen species metabolic process superoxide metabolic process positive regulation of metabolic process superoxide anion generation metabolic process cellular process positive regulation of superoxide anion generation regulation of superoxide anion generation regulation of metabolic process regulation of reactive oxygen species metabolic process positive regulation of cellular process multicellular organismal process inner ear receptor cell development cell projection organization sensory organ development epidermis development auditory receptor cell stereocilium organization neuron projection development epithelial cell differentiation hair cell differentiation multicellular organism development neuron differentiation cell differentiation inner ear development anatomical structure development animal organ morphogenesis system development developmental process embryonic organ morphogenesis mechanoreceptor differentiation epithelium development epidermal cell differentiation ear development embryonic morphogenesis nervous system development tissue development inner ear receptor cell differentiation generation of neurons auditory receptor cell development cellular developmental process cell development embryo development cell morphogenesis cellular component organization neurogenesis cellular component organization or biogenesis auditory receptor cell morphogenesis embryonic organ development ear morphogenesis plasma membrane bounded cell projection organization animal organ development inner ear auditory receptor cell differentiation cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis sensory organ morphogenesis neuron development inner ear morphogenesis inner ear receptor cell stereocilium organization system process circulatory system process regulation of blood pressure regulation of biological quality blood circulation spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation response to organic substance cellular localization anterograde axonal transport transport intracellular transport axonal transport establishment of localization localization axo-dendritic transport establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process placenta development regulation of system process negative regulation of biological process negative regulation of muscle contraction smooth muscle contraction regulation of smooth muscle contraction regulation of multicellular organismal process blood vessel diameter maintenance negative regulation of smooth muscle contraction regulation of tube diameter relaxation of smooth muscle regulation of tube size muscle contraction muscle system process regulation of muscle system process relaxation of muscle relaxation of vascular associated smooth muscle regulation of muscle contraction vascular process in circulatory system negative regulation of multicellular organismal process vasodilation regulation of anatomical structure size apoptotic process cell death programmed cell death positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death positive regulation of apoptotic process cellular response to stimulus positive regulation of cell communication intrinsic apoptotic signaling pathway in response to oxidative stress positive regulation of signal transduction regulation of oxidative stress-induced intrinsic apoptotic signaling pathway signaling regulation of signal transduction regulation of intrinsic apoptotic signaling pathway intracellular signal transduction cell communication positive regulation of apoptotic signaling pathway positive regulation of response to stimulus regulation of intracellular signal transduction signal transduction intrinsic apoptotic signaling pathway regulation of signaling positive regulation of intracellular signal transduction apoptotic signaling pathway regulation of response to stimulus positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway regulation of cell communication positive regulation of intrinsic apoptotic signaling pathway regulation of apoptotic signaling pathway positive regulation of signaling regulation of localization import into cell positive regulation of cellular component organization regulation of cellular component organization vesicle-mediated transport positive regulation of endocytosis phagocytosis regulation of endocytosis regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport positive regulation of phagocytosis positive regulation of transport endocytosis glutathione metabolic process organonitrogen compound metabolic process organic substance metabolic process sulfur compound metabolic process amide metabolic process cellular modified amino acid metabolic process negative regulation of small molecule metabolic process regulation of cholesterol metabolic process regulation of lipid metabolic process sterol metabolic process negative regulation of lipid biosynthetic process regulation of primary metabolic process regulation of small molecule metabolic process organic substance biosynthetic process small molecule metabolic process negative regulation of steroid metabolic process regulation of alcohol biosynthetic process negative regulation of metabolic process primary metabolic process organic cyclic compound metabolic process biosynthetic process sterol biosynthetic process organic cyclic compound biosynthetic process regulation of sterol biosynthetic process negative regulation of alcohol biosynthetic process negative regulation of lipid metabolic process regulation of cholesterol biosynthetic process regulation of steroid biosynthetic process negative regulation of cholesterol metabolic process steroid metabolic process organic hydroxy compound metabolic process cholesterol metabolic process lipid biosynthetic process alcohol metabolic process steroid biosynthetic process regulation of biosynthetic process secondary alcohol biosynthetic process small molecule biosynthetic process regulation of steroid metabolic process cholesterol biosynthetic process negative regulation of sterol biosynthetic process secondary alcohol metabolic process negative regulation of biosynthetic process organic hydroxy compound biosynthetic process alcohol biosynthetic process negative regulation of steroid biosynthetic process regulation of lipid biosynthetic process negative regulation of cholesterol biosynthetic process lipid metabolic process regulation of multicellular organism growth regulation of growth regulation of developmental growth regulation of developmental process developmental growth growth multicellular organism growth action potential initiation action potential regulation of membrane potential negative regulation of reproductive process regulation of reproductive process gonad development reproductive system development female gonad development sex differentiation female sex differentiation development of primary female sexual characteristics development of primary sexual characteristics reproductive structure development ovarian follicle development nervous system process transmission of nerve impulse sensory perception sensory perception of sound sensory perception of mechanical stimulus programmed cell death involved in cell development ectopic germ cell programmed cell death reactive oxygen species biosynthetic process cellular biosynthetic process hydrogen peroxide metabolic process hydrogen peroxide biosynthetic process regulation of molecular function regulation of catalytic activity regulation of hydrolase activity regulation of GTPase activity regulation of protein modification process regulation of protein phosphorylation regulation of transferase activity regulation of phosphate metabolic process phosphate-containing compound metabolic process protein metabolic process phosphorus metabolic process protein modification process protein phosphorylation phosphorylation regulation of protein metabolic process regulation of protein kinase activity regulation of macromolecule metabolic process regulation of kinase activity macromolecule modification regulation of phosphorylation regulation of phosphorus metabolic process macromolecule metabolic process response to hydrogen peroxide response to oxidative stress response to oxygen-containing compound response to reactive oxygen species response to inorganic substance peripheral nervous system axon ensheathment glial cell development gliogenesis axon ensheathment ensheathment of neurons plasma membrane organization myelination in peripheral nervous system peripheral nervous system myelin maintenance Schwann cell differentiation endomembrane system organization membrane organization peripheral nervous system development myelination Schwann cell development glial cell differentiation myelin maintenance response to heat response to abiotic stimulus response to temperature stimulus muscle cell cellular homeostasis behavior locomotory behavior immune system development gland development hematopoietic or lymphoid organ development thymus development immune system process multicellular organismal-level homeostasis anatomical structure homeostasis tissue homeostasis retina homeostasis cellular response to oxidative stress detoxification 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 cellular detoxification cellular response to oxygen-containing compound response to toxic substance removal of superoxide radicals cellular response to chemical stimulus cellular response to superoxide cellular response to toxic substance response to oxygen radical regulation of mitochondrial membrane potential regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response negative regulation of response to stimulus response to external stimulus regulation of inflammatory response negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death negative regulation of apoptotic process negative regulation of cellular process regulation of neuron apoptotic process negative regulation of developmental process multi-multicellular organism process female pregnancy embryo implantation multi-organism reproductive process response to alcohol response to ethanol heart process heart contraction neuronal action potential organ growth regulation of organ growth homeostasis of number of cells myeloid cell homeostasis intracellular signaling cassette positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade determination of adult lifespan gene expression macromolecule biosynthetic process regulation of leukocyte differentiation regulation of leukocyte activation regulation of cell activation regulation of T cell differentiation in thymus mononuclear cell differentiation regulation of cell differentiation lymphocyte activation lymphocyte differentiation regulation of cell development leukocyte activation regulation of T cell differentiation T cell differentiation in thymus T cell activation T cell differentiation regulation of immune system process regulation of lymphocyte differentiation regulation of multicellular organismal development hemopoiesis cell activation regulation of T cell activation regulation of hemopoiesis leukocyte differentiation regulation of lymphocyte activation positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process cytokine production regulation of cytokine production positive regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process positive regulation of cytokine production positive regulation of cellular biosynthetic process positive regulation of molecular function positive regulation of catalytic activity retrograde axonal transport intermediate filament-based process organelle organization neurofilament cytoskeleton organization cytoskeleton organization intermediate filament cytoskeleton organization	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular organelle extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular organelle peroxisome microbody intracellular membrane-bounded organelle somatodendritic compartment cell body neuronal cell body mitochondrial intermembrane space mitochondrion membrane-enclosed lumen intracellular organelle lumen organelle envelope lumen organelle envelope organelle lumen mitochondrial envelope neuron projection cytoplasm axon axon cytoplasm neuron projection cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection cell projection nucleus nucleoplasm nuclear lumen protein-containing complex dendrite cytoplasm dendrite dendritic tree cytoplasmic vesicle intracellular vesicle mitochondrial matrix
B, D	Superoxide dismutase 1 copper chaperone	superoxide dismutase copper chaperone activity metallochaperone activity molecular carrier activity copper chaperone activity cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding	organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process protein maturation by copper ion transfer primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process biosynthetic process organic substance biosynthetic process metabolic process cellular process protein metabolic process organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process protein maturation by copper ion transfer primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process biosynthetic process organic substance biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process 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 response to inorganic substance 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 cellular response to toxic substance response to oxygen radical localization transport copper ion transport transition metal ion transport monoatomic ion transport monoatomic cation transport establishment of localization metal ion transport	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope organelle membrane protein-containing complex protein folding chaperone complex intracellular protein-containing complex catalytic complex oxidoreductase complex superoxide dismutase complex cytosol mitochondrial intermembrane space membrane-enclosed lumen intracellular organelle lumen organelle envelope lumen organelle lumen nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR024134	Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone	Family
A, C	IPR036423	Superoxide dismutase-like, copper/zinc binding domain superfamily	Homologous Superfamily
A, C	IPR018152	Superoxide dismutase, copper/zinc, binding site	Binding Site
A, C	IPR001424	Superoxide dismutase, copper/zinc binding domain	Domain
B, D	IPR024134	Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone	Family
B, D	IPR006121	Heavy metal-associated domain, HMA	Domain
B, D	IPR036423	Superoxide dismutase-like, copper/zinc binding domain superfamily	Homologous Superfamily
B, D	IPR036163	Heavy metal-associated domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: P00441	amyotrophic lateral sclerosis amyotrophic lateral sclerosis type 1 perinatal asphyxia hyperthyroidism myelomeningocele Down syndrome muscular atrophy retinal degeneration scrapie diabetic retinopathy Turner syndrome malignant glioma Marfan syndrome MELAS syndrome type 2 diabetes mellitus amyotrophic lateral sclerosis amyotrophic lateral sclerosis type 1 perinatal asphyxia hyperthyroidism myelomeningocele Down syndrome muscular atrophy retinal degeneration scrapie diabetic retinopathy Turner syndrome malignant glioma Marfan syndrome MELAS syndrome type 2 diabetes mellitus progressive external ophthalmoplegia motor neuron disease pulmonary fibrosis congestive heart failure Necrosis obesity disorder hearing loss disorder atherosclerosis brain ischemia melancholia contact dermatitis iron deficiency anemia nervous system disorder diabetes mellitus ovarian cancer asthma liver disease Parkinson disease endogenous depression mixed glioma proteinuria hypertensive disorder myocardial infarction intestinal schistosomiasis nephrosis neurodegenerative disease aortic disease transient ischemic attack lateral sclerosis ovarian neoplasm heart failure maturity-onset diabetes of the young drug-induced liver injury fatty liver disease alcoholic fatty liver disease schizophrenia idiopathic interstitial pneumonia dementia ischemia reperfusion injury glioma arteriosclerosis disorder pancreatic ductal adenocarcinoma lymphoplasmacytic lymphoma plasma cell myeloma hepatitis fetal growth restriction ischemic disease neurotic disorder anterior horn disease bipolar disorder primary ovarian failure cerebrovascular disorder acute kidney failure hypotensive disorder spinal cord injury depressive disorder juvenile primary lateral sclerosis nutritional deficiency disease

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.