1Q0K

Crystal structure of Ni-containing superoxide dismutase with Ni-ligation corresponding to the thiosulfate-reduced state

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)
A	d1q0ka_	All alpha proteins	Four-helical up-and-down bundle	Nickel-containing superoxide dismutase, NiSOD	Nickel-containing superoxide dismutase, NiSOD	Nickel-containing superoxide dismutase, NiSOD	(Streptomyces seoulensis ) [TaxId: 73044 ],	SCOPe (2.08)
B	d1q0kb_	All alpha proteins	Four-helical up-and-down bundle	Nickel-containing superoxide dismutase, NiSOD	Nickel-containing superoxide dismutase, NiSOD	Nickel-containing superoxide dismutase, NiSOD	(Streptomyces seoulensis ) [TaxId: 73044 ],	SCOPe (2.08)
E	d1q0ke_	All alpha proteins	Four-helical up-and-down bundle	Nickel-containing superoxide dismutase, NiSOD	Nickel-containing superoxide dismutase, NiSOD	Nickel-containing superoxide dismutase, NiSOD	(Streptomyces seoulensis ) [TaxId: 73044 ],	SCOPe (2.08)
F	d1q0kf_	All alpha proteins	Four-helical up-and-down bundle	Nickel-containing superoxide dismutase, NiSOD	Nickel-containing superoxide dismutase, NiSOD	Nickel-containing superoxide dismutase, NiSOD	(Streptomyces seoulensis ) [TaxId: 73044 ],	SCOPe (2.08)
K	d1q0kk_	All alpha proteins	Four-helical up-and-down bundle	Nickel-containing superoxide dismutase, NiSOD	Nickel-containing superoxide dismutase, NiSOD	Nickel-containing superoxide dismutase, NiSOD	(Streptomyces seoulensis ) [TaxId: 73044 ],	SCOPe (2.08)
C	d1q0kc_	All alpha proteins	Four-helical up-and-down bundle	Nickel-containing superoxide dismutase, NiSOD	Nickel-containing superoxide dismutase, NiSOD	Nickel-containing superoxide dismutase, NiSOD	(Streptomyces seoulensis ) [TaxId: 73044 ],	SCOPe (2.08)
D	d1q0kd_	All alpha proteins	Four-helical up-and-down bundle	Nickel-containing superoxide dismutase, NiSOD	Nickel-containing superoxide dismutase, NiSOD	Nickel-containing superoxide dismutase, NiSOD	(Streptomyces seoulensis ) [TaxId: 73044 ],	SCOPe (2.08)
G	d1q0kg_	All alpha proteins	Four-helical up-and-down bundle	Nickel-containing superoxide dismutase, NiSOD	Nickel-containing superoxide dismutase, NiSOD	Nickel-containing superoxide dismutase, NiSOD	(Streptomyces seoulensis ) [TaxId: 73044 ],	SCOPe (2.08)
H	d1q0kh_	All alpha proteins	Four-helical up-and-down bundle	Nickel-containing superoxide dismutase, NiSOD	Nickel-containing superoxide dismutase, NiSOD	Nickel-containing superoxide dismutase, NiSOD	(Streptomyces seoulensis ) [TaxId: 73044 ],	SCOPe (2.08)
I	d1q0ki_	All alpha proteins	Four-helical up-and-down bundle	Nickel-containing superoxide dismutase, NiSOD	Nickel-containing superoxide dismutase, NiSOD	Nickel-containing superoxide dismutase, NiSOD	(Streptomyces seoulensis ) [TaxId: 73044 ],	SCOPe (2.08)
J	d1q0kj_	All alpha proteins	Four-helical up-and-down bundle	Nickel-containing superoxide dismutase, NiSOD	Nickel-containing superoxide dismutase, NiSOD	Nickel-containing superoxide dismutase, NiSOD	(Streptomyces seoulensis ) [TaxId: 73044 ],	SCOPe (2.08)
L	d1q0kl_	All alpha proteins	Four-helical up-and-down bundle	Nickel-containing superoxide dismutase, NiSOD	Nickel-containing superoxide dismutase, NiSOD	Nickel-containing superoxide dismutase, NiSOD	(Streptomyces seoulensis ) [TaxId: 73044 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nickel-containing superoxide dismutase NiSOD	8038385	3001167	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nickel-containing superoxide dismutase NiSOD	8038385	3001167	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Nickel-containing superoxide dismutase NiSOD	8038385	3001167	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Nickel-containing superoxide dismutase NiSOD	8038385	3001167	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Nickel-containing superoxide dismutase NiSOD	8038385	3001167	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nickel-containing superoxide dismutase NiSOD	8038385	3001167	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nickel-containing superoxide dismutase NiSOD	8038385	3001167	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Nickel-containing superoxide dismutase NiSOD	8038385	3001167	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Nickel-containing superoxide dismutase NiSOD	8038385	3001167	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Nickel-containing superoxide dismutase NiSOD	8038385	3001167	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Nickel-containing superoxide dismutase NiSOD	8038385	3001167	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Nickel-containing superoxide dismutase NiSOD	8038385	3001167	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	Sod_Ni	e1q0kA1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Nickel-containing superoxide dismutase, NiSOD (From Topology)	T: Nickel-containing superoxide dismutase, NiSOD	F: Sod_Ni	ECOD (1.6)
B	Sod_Ni	e1q0kB1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Nickel-containing superoxide dismutase, NiSOD (From Topology)	T: Nickel-containing superoxide dismutase, NiSOD	F: Sod_Ni	ECOD (1.6)
E	Sod_Ni	e1q0kE1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Nickel-containing superoxide dismutase, NiSOD (From Topology)	T: Nickel-containing superoxide dismutase, NiSOD	F: Sod_Ni	ECOD (1.6)
F	Sod_Ni	e1q0kF1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Nickel-containing superoxide dismutase, NiSOD (From Topology)	T: Nickel-containing superoxide dismutase, NiSOD	F: Sod_Ni	ECOD (1.6)
K	Sod_Ni	e1q0kK1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Nickel-containing superoxide dismutase, NiSOD (From Topology)	T: Nickel-containing superoxide dismutase, NiSOD	F: Sod_Ni	ECOD (1.6)
C	Sod_Ni	e1q0kC1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Nickel-containing superoxide dismutase, NiSOD (From Topology)	T: Nickel-containing superoxide dismutase, NiSOD	F: Sod_Ni	ECOD (1.6)
D	Sod_Ni	e1q0kD1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Nickel-containing superoxide dismutase, NiSOD (From Topology)	T: Nickel-containing superoxide dismutase, NiSOD	F: Sod_Ni	ECOD (1.6)
G	Sod_Ni	e1q0kG1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Nickel-containing superoxide dismutase, NiSOD (From Topology)	T: Nickel-containing superoxide dismutase, NiSOD	F: Sod_Ni	ECOD (1.6)
H	Sod_Ni	e1q0kH1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Nickel-containing superoxide dismutase, NiSOD (From Topology)	T: Nickel-containing superoxide dismutase, NiSOD	F: Sod_Ni	ECOD (1.6)
I	Sod_Ni	e1q0kI1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Nickel-containing superoxide dismutase, NiSOD (From Topology)	T: Nickel-containing superoxide dismutase, NiSOD	F: Sod_Ni	ECOD (1.6)
J	Sod_Ni	e1q0kJ1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Nickel-containing superoxide dismutase, NiSOD (From Topology)	T: Nickel-containing superoxide dismutase, NiSOD	F: Sod_Ni	ECOD (1.6)
L	Sod_Ni	e1q0kL1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Nickel-containing superoxide dismutase, NiSOD (From Topology)	T: Nickel-containing superoxide dismutase, NiSOD	F: Sod_Ni	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.120.400	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Nickel-containing superoxide dismutase	CATH (4.3.0)
B	1.20.120.400	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Nickel-containing superoxide dismutase	CATH (4.3.0)
E	1.20.120.400	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Nickel-containing superoxide dismutase	CATH (4.3.0)
F	1.20.120.400	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Nickel-containing superoxide dismutase	CATH (4.3.0)
K	1.20.120.400	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Nickel-containing superoxide dismutase	CATH (4.3.0)
C	1.20.120.400	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Nickel-containing superoxide dismutase	CATH (4.3.0)
D	1.20.120.400	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Nickel-containing superoxide dismutase	CATH (4.3.0)
G	1.20.120.400	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Nickel-containing superoxide dismutase	CATH (4.3.0)
H	1.20.120.400	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Nickel-containing superoxide dismutase	CATH (4.3.0)
I	1.20.120.400	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Nickel-containing superoxide dismutase	CATH (4.3.0)
J	1.20.120.400	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Nickel-containing superoxide dismutase	CATH (4.3.0)
L	1.20.120.400	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Nickel-containing superoxide dismutase	CATH (4.3.0)

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	PF09055	Nickel-containing superoxide dismutase (Sod_Ni)	Nickel-containing superoxide dismutase	Nickel containing superoxide dismutase (NiSOD) is a metalloenzyme containing a hexameric assembly of right-handed 4-helix bundles of up-down-up-down topology with an N-terminal His-Cys-X-X-Pro-Cys-Gly-X-Tyr motif that chelates the active site Ni ions ...	Nickel containing superoxide dismutase (NiSOD) is a metalloenzyme containing a hexameric assembly of right-handed 4-helix bundles of up-down-up-down topology with an N-terminal His-Cys-X-X-Pro-Cys-Gly-X-Tyr motif that chelates the active site Ni ions. NiSOD catalyses the disproportionation of superoxide to peroxide and molecular oxygen through alternate oxidation and reduction of Ni, protecting cells from the toxic products of aerobic metabolism [1].	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	Superoxide dismutase [Ni]	cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding superoxide dismutase activity oxidoreductase activity, acting on superoxide radicals as acceptor oxidoreductase activity antioxidant activity catalytic activity	-	intracellular anatomical structure cytoplasm cellular anatomical entity

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	IPR036502	Nickel-containing superoxide dismutase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR014123	Superoxide dismutase, Nickel-type	Family

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.