8IQ0 | pdb_00008iq0

Crystal structure of hydrogen sulfide-bound superoxide dismutase in oxidized state

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
P	SCOP2B Superfamily	Cu, Zn superoxide dismutase-like	8055251	3002059	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Cu, Zn superoxide dismutase-like	8055251	3002059	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Cu, Zn superoxide dismutase-like	8055251	3002059	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Cu, Zn superoxide dismutase-like	8055251	3002059	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Cu, Zn superoxide dismutase-like	8055251	3002059	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Cu, Zn superoxide dismutase-like	8055251	3002059	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Cu, Zn superoxide dismutase-like	8055251	3002059	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Cu, Zn superoxide dismutase-like	8055251	3002059	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Cu, Zn superoxide dismutase-like	8055251	3002059	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Cu, Zn superoxide dismutase-like	8055251	3002059	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Cu, Zn superoxide dismutase-like	8055251	3002059	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Cu, Zn superoxide dismutase-like	8055251	3002059	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cu, Zn superoxide dismutase-like	8055251	3002059	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cu, Zn superoxide dismutase-like	8055251	3002059	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cu, Zn superoxide dismutase-like	8055251	3002059	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cu, Zn superoxide dismutase-like	8055251	3002059	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)
P	Cullin_AB	e8iq0P1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
O	Cullin_AB	e8iq0O1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
N	Cullin_AB	e8iq0N1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
M	Cullin_AB	e8iq0M1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
L	Cullin_AB	e8iq0L1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
K	Cullin_AB	e8iq0K1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
J	Cullin_AB	e8iq0J1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
I	Cullin_AB	e8iq0I1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
H	Cullin_AB	e8iq0H1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
G	Cullin_AB	e8iq0G1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
F	Cullin_AB	e8iq0F1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
E	Cullin_AB	e8iq0E1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
D	Cullin_AB	e8iq0D1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
C	Cullin_AB	e8iq0C1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
B	Cullin_AB	e8iq0B1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
A	SPRY,PRY	e8iq0A1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: SPRY,PRY	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
P	2.60.40.200	Mainly Beta	Sandwich	Immunoglobulin-like	Superoxide dismutase, copper/zinc binding domain	CATH (utative)
O	2.60.40.200	Mainly Beta	Sandwich	Immunoglobulin-like	Superoxide dismutase, copper/zinc binding domain	CATH (utative)
N	2.60.40.200	Mainly Beta	Sandwich	Immunoglobulin-like	Superoxide dismutase, copper/zinc binding domain	CATH (utative)
M	2.60.40.200	Mainly Beta	Sandwich	Immunoglobulin-like	Superoxide dismutase, copper/zinc binding domain	CATH (utative)
L	2.60.40.200	Mainly Beta	Sandwich	Immunoglobulin-like	Superoxide dismutase, copper/zinc binding domain	CATH (utative)
K	2.60.40.200	Mainly Beta	Sandwich	Immunoglobulin-like	Superoxide dismutase, copper/zinc binding domain	CATH (utative)
J	2.60.40.200	Mainly Beta	Sandwich	Immunoglobulin-like	Superoxide dismutase, copper/zinc binding domain	CATH (utative)
I	2.60.40.200	Mainly Beta	Sandwich	Immunoglobulin-like	Superoxide dismutase, copper/zinc binding domain	CATH (utative)
H	2.60.40.200	Mainly Beta	Sandwich	Immunoglobulin-like	Superoxide dismutase, copper/zinc binding domain	CATH (utative)
G	2.60.40.200	Mainly Beta	Sandwich	Immunoglobulin-like	Superoxide dismutase, copper/zinc binding domain	CATH (utative)
F	2.60.40.200	Mainly Beta	Sandwich	Immunoglobulin-like	Superoxide dismutase, copper/zinc binding domain	CATH (utative)
E	2.60.40.200	Mainly Beta	Sandwich	Immunoglobulin-like	Superoxide dismutase, copper/zinc binding domain	CATH (utative)
D	2.60.40.200	Mainly Beta	Sandwich	Immunoglobulin-like	Superoxide dismutase, copper/zinc binding domain	CATH (utative)
C	2.60.40.200	Mainly Beta	Sandwich	Immunoglobulin-like	Superoxide dismutase, copper/zinc binding domain	CATH (utative)
B	2.60.40.200	Mainly Beta	Sandwich	Immunoglobulin-like	Superoxide dismutase, copper/zinc binding domain	CATH (utative)
A	2.60.40.200	Mainly Beta	Sandwich	Immunoglobulin-like	Superoxide dismutase, copper/zinc binding domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	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 SOD ...	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	Superoxide dismutase [Cu-Zn]	cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding protein binding protein-folding chaperone binding protein phosphatase binding phosphatase binding protein phosphatase 2B binding enzyme binding superoxide dismutase activity cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding protein binding protein-folding chaperone binding protein phosphatase binding phosphatase binding protein phosphatase 2B binding enzyme binding superoxide dismutase activity oxidoreductase activity, acting on superoxide radicals as acceptor oxidoreductase activity antioxidant activity catalytic activity identical protein binding protein homodimerization activity protein dimerization activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity ubiquitin-protein transferase 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 stress response to wounding response to axon injury 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 stress response to wounding response to axon injury 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 cellular process inner ear receptor cell stereocilium organization system process circulatory system process regulation of blood pressure biological regulation 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 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 regulation of biological process 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 glutathione metabolic process modified amino acid metabolic process sulfur compound metabolic process metabolic process regulation of multicellular organism growth regulation of growth regulation of developmental growth regulation of developmental process developmental growth growth multicellular organism growth protein polyubiquitination primary metabolic process protein ubiquitination macromolecule modification protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal 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 cell communication sensory perception sensory perception of sound sensory perception of mechanical stimulus reactive oxygen species biosynthetic process biosynthetic process reactive oxygen species metabolic process hydrogen peroxide metabolic process hydrogen peroxide biosynthetic process response to hydrogen peroxide response to oxidative stress response to chemical response to oxygen-containing compound response to reactive oxygen species 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 multicellular organismal-level homeostasis anatomical structure homeostasis tissue homeostasis retina homeostasis cellular response to stimulus 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 superoxide metabolic process 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 membrane potential neuron apoptotic process regulation of cellular process negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death regulation of neuron apoptotic process catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process multi-multicellular organism process female pregnancy embryo implantation multi-organism reproductive process response to alcohol response to ethanol heart process heart contraction immune system process homeostasis of number of cells myeloid cell homeostasis positive regulation of cell communication positive regulation of signal transduction signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of signaling positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication positive regulation of signaling positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process cytokine production regulation of cytokine production positive regulation of macromolecule metabolic process regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule 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 regulation of metabolic process positive regulation of molecular function regulation of molecular function regulation of catalytic activity positive regulation of catalytic activity intermediate filament-based process organelle organization neurofilament cytoskeleton organization cytoskeleton organization intermediate filament cytoskeleton organization	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle peroxisome microbody intracellular membrane-bounded organelle somatodendritic compartment cell body neuronal cell body mitochondrion cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle peroxisome microbody intracellular membrane-bounded organelle somatodendritic compartment cell body neuronal cell body mitochondrion protein-containing complex neuron projection cytoplasm neuron projection plasma membrane bounded cell projection dendrite cytoplasm cell projection dendrite dendritic tree cytoplasmic vesicle intracellular vesicle vesicle nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR024134	Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR036423	Superoxide dismutase-like, copper/zinc binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR018152	Superoxide dismutase, copper/zinc, binding site	Binding Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR001424	Superoxide dismutase, copper/zinc binding domain	Domain

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.