Annotations: 3L9E

Crystal structures of holo and Cu-deficient Cu/ZnSOD from the silkworm Bombyx mori and the implications in Amyotrophic lateral sclerosis

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	d3l9ed_	All beta proteins	Immunoglobulin-like beta-sandwich	Cu,Zn superoxide dismutase-like	Cu,Zn superoxide dismutase-like	Cu,Zn superoxide dismutase, SOD	Silk moth (Bombyx mori ) [TaxId: 7091 ],	SCOPe (2.08)
C	d3l9ec_	All beta proteins	Immunoglobulin-like beta-sandwich	Cu,Zn superoxide dismutase-like	Cu,Zn superoxide dismutase-like	Cu,Zn superoxide dismutase, SOD	Silk moth (Bombyx mori ) [TaxId: 7091 ],	SCOPe (2.08)
B	d3l9eb_	All beta proteins	Immunoglobulin-like beta-sandwich	Cu,Zn superoxide dismutase-like	Cu,Zn superoxide dismutase-like	Cu,Zn superoxide dismutase, SOD	Silk moth (Bombyx mori ) [TaxId: 7091 ],	SCOPe (2.08)
A	d3l9ea_	All beta proteins	Immunoglobulin-like beta-sandwich	Cu,Zn superoxide dismutase-like	Cu,Zn superoxide dismutase-like	Cu,Zn superoxide dismutase, SOD	Silk moth (Bombyx mori ) [TaxId: 7091 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Cu, Zn superoxide dismutase-like	8062193	3002059	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cu, Zn superoxide dismutase-like	8062193	3002059	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cu, Zn superoxide dismutase-like	8062193	3002059	SCOP2B (2022-06-29)
A	SCOP2 Family	Cu, Zn superoxide dismutase-like	8062192	4007548	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cu, Zn superoxide dismutase-like	8062193	3002059	SCOP2 (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	RVP	e3l9eD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.2)
C	RVP	e3l9eC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.2)
B	RVP	e3l9eB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.2)
A	Pyrophosphatase	e3l9eA1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: sensor domains	T: sensor domains	F: Pyrophosphatase	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.60.40.200	Mainly Beta	Sandwich	Immunoglobulin-like	Superoxide dismutase, copper/zinc binding domain	CATH (4.3.0)
C	2.60.40.200	Mainly Beta	Sandwich	Immunoglobulin-like	Superoxide dismutase, copper/zinc binding domain	CATH (4.3.0)
B	2.60.40.200	Mainly Beta	Sandwich	Immunoglobulin-like	Superoxide dismutase, copper/zinc binding domain	CATH (4.3.0)
A	2.60.40.200	Mainly Beta	Sandwich	Immunoglobulin-like	Superoxide dismutase, copper/zinc binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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	Superoxide dismutase [Cu-Zn]	cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding zinc ion binding identical protein binding protein binding superoxide dismutase activity oxidoreductase activity, acting on superoxide radicals as acceptor oxidoreductase activity antioxidant activity cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding zinc ion binding identical protein binding protein binding superoxide dismutase activity oxidoreductase activity, acting on superoxide radicals as acceptor oxidoreductase activity antioxidant activity catalytic activity	-	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

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

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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.