6ADQ | pdb_00006adq

Respiratory Complex CIII2CIV2SOD2 from Mycobacterium smegmatis

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
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
T [auth Z]	SCOP2B Superfamily	Cu, Zn superoxide dismutase-like	8083885	3002059	SCOP2B (2022-06-29)
H [auth Y]	SCOP2 Family	Cu, Zn superoxide dismutase-like	8083884	4007548	SCOP2 (2022-06-29)
H [auth Y]	SCOP2 Superfamily	Cu, Zn superoxide dismutase-like	8083885	3002059	SCOP2 (2022-06-29)
O [auth S]	SCOP2B Superfamily	Cytochrome c oxidase subunit III-like	8075786	3000671	SCOP2B (2022-06-29)
C [auth G]	SCOP2B Superfamily	Cytochrome c oxidase subunit III-like	8075786	3000671	SCOP2B (2022-06-29)
N [auth R]	SCOP2 Family	Cytochrome c oxidase subunit I-like	8096163	4001989	SCOP2 (2022-06-29)
N [auth R]	SCOP2 Superfamily	Cytochrome c oxidase subunit I-like	8096164	3000653	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)
U [auth W]	UNK_F_TYPE	e6adqW1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: UNK_F_TYPE	ECOD (1.6)
I [auth K]	UNK_F_TYPE	e6adqK1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: UNK_F_TYPE	ECOD (1.6)
R [auth V]	TPM_phosphatase	e6adqV1	A: a+b three layers	X: thylakoid acid phosphatase domain-related (From Topology)	H: thylakoid acid phosphatase domain-related (From Topology)	T: thylakoid acid phosphatase domain-related	F: TPM_phosphatase	ECOD (1.6)
F [auth J]	TPM_phosphatase	e6adqJ1	A: a+b three layers	X: thylakoid acid phosphatase domain-related (From Topology)	H: thylakoid acid phosphatase domain-related (From Topology)	T: thylakoid acid phosphatase domain-related	F: TPM_phosphatase	ECOD (1.6)
O [auth S]	COX3	e6adqS1	A: alpha bundles	X: Cytochrome c oxidase subunit III-like (From Topology)	H: Cytochrome c oxidase subunit III-like (From Topology)	T: Cytochrome c oxidase subunit III-like	F: COX3	ECOD (1.6)
C [auth G]	COX3	e6adqG1	A: alpha bundles	X: Cytochrome c oxidase subunit III-like (From Topology)	H: Cytochrome c oxidase subunit III-like (From Topology)	T: Cytochrome c oxidase subunit III-like	F: COX3	ECOD (1.6)
N [auth R]	COX1	e6adqR1	A: alpha superhelices	X: Cytochrome c oxidase subunit I-like	H: Cytochrome c oxidase subunit I-like (From Topology)	T: Cytochrome c oxidase subunit I-like	F: COX1	ECOD (1.6)
B [auth F]	COX1	e6adqF1	A: alpha superhelices	X: Cytochrome c oxidase subunit I-like	H: Cytochrome c oxidase subunit I-like (From Topology)	T: Cytochrome c oxidase subunit I-like	F: COX1	ECOD (1.6)
M [auth Q]	COX2	e6adqQ2	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: COX2	ECOD (1.6)
M [auth Q]	COX2_TM_1	e6adqQ1	A: extended segments	X: Cytochrome c oxidase subunit II-like, transmembrane region (From Topology)	H: Cytochrome c oxidase subunit II-like, transmembrane region (From Topology)	T: Cytochrome c oxidase subunit II-like, transmembrane region	F: COX2_TM_1	ECOD (1.6)
A [auth E]	COX2	e6adqE1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: COX2	ECOD (1.6)
A [auth E]	COX2_TM_1	e6adqE2	A: extended segments	X: Cytochrome c oxidase subunit II-like, transmembrane region (From Topology)	H: Cytochrome c oxidase subunit II-like, transmembrane region (From Topology)	T: Cytochrome c oxidase subunit II-like, transmembrane region	F: COX2_TM_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth G]	1.20.120.80	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Cytochrome c oxidase, subunit III, four-helix bundle	CATH (utative)
N [auth R]	1.20.210.10	Mainly Alpha	Up-down Bundle	Cytochrome C Oxidase	Chain A	CATH (utative)
B [auth F]	1.20.210.10	Mainly Alpha	Up-down Bundle	Cytochrome C Oxidase	Chain A	CATH (utative)
V [auth N]	1.20.810.10	Mainly Alpha	Up-down Bundle	Cytochrome Bc1 Complex	Chain C	CATH (utative)
J [auth B]	1.20.810.10	Mainly Alpha	Up-down Bundle	Cytochrome Bc1 Complex	Chain C	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
H [auth Y], T [auth Z]	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
F [auth J], R [auth V]	PF17174	Domain of unknown function (DUF5130) (DUF5130)	Domain of unknown function (DUF5130)	-	Family
D [auth H], P [auth T]	PF12270	Cytochrome c oxidase subunit IV (Cyt_c_ox_IV)	Cytochrome c oxidase subunit IV	-	Family
C [auth G], O [auth S]	PF00510	Cytochrome c oxidase subunit III (COX3)	Cytochrome c oxidase subunit III		Domain
L [auth A], X [auth M]	PF00355	Rieske [2Fe-2S] domain (Rieske)	Rieske [2Fe-2S] domain	The rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in ...	The rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in this motif form a disulphide bridge, which stabilises the protein [4].	Domain
K [auth C], W [auth O]	PF13442	Cytochrome C oxidase, cbb3-type, subunit III (Cytochrome_CBB3)	Cytochrome C oxidase, cbb3-type, subunit III		Domain
K [auth C], W [auth O]	PF00034	Cytochrome c (Cytochrom_C)	Cytochrome c	The Pfam entry does not include all Prosite members. The cytochrome 556 and cytochrome c' families are not included. All these are now in a new clan together. The C-terminus of DUF989, Pfam:PF06181, has now been merged into this family.	Domain
J [auth B], V [auth N]	PF13631	Cytochrome b(N-terminal)/b6/petB (Cytochrom_B_N_2)	Cytochrome b(N-terminal)/b6/petB		Domain
A [auth E], M [auth Q]	PF00116	Cytochrome C oxidase subunit II, periplasmic domain (COX2)	Cytochrome C oxidase subunit II, periplasmic domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I [auth K], U [auth W]	LpqE protein	-	-	-
H [auth Y], T [auth Z]	Superoxide dismutase [Cu-Zn]	cation binding ion binding binding metal ion binding small molecule binding superoxide dismutase activity oxidoreductase activity, acting on superoxide radicals as acceptor oxidoreductase activity antioxidant activity catalytic activity	-	-
G [auth D], S [auth P]	Prokaryotic respiratory supercomplex associate factor 1 PRSAF1	-	-	cellular anatomical structure membrane
F [auth J], R [auth V]	Uncharacterized protein MSMEG_4692/MSMEI_4575	-	-	-
E [auth I], Q [auth U]	Cytochrome c oxidase subunit CtaJ	-	-	cellular anatomical structure membrane
D [auth H], P [auth T]	Cytochrome c oxidase polypeptide 4	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity	electron transport chain metabolic process cellular process generation of precursor metabolites and energy	cell periphery cellular anatomical structure plasma membrane membrane
C [auth G], O [auth S]	Cytochrome c oxidase subunit 3	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity	aerobic electron transport chain aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy	cell periphery cellular anatomical structure plasma membrane membrane
B [auth F], N [auth R]	Cytochrome c oxidase subunit 1	-	-	-
L [auth A], X [auth M]	Rieske iron-sulfur protein QcrA	monooxygenase activity oxidoreductase activity catalytic activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	-	cell periphery cellular anatomical structure plasma membrane membrane
K [auth C], W [auth O]	Cytochrome bc1 complex cytochrome c subunit	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity quinol-cytochrome-c reductase activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity binding tetrapyrrole binding heme binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity quinol-cytochrome-c reductase activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity binding tetrapyrrole binding heme binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding	-	cell periphery cellular anatomical structure plasma membrane membrane
J [auth B], V [auth N]	Ubiquinol-cytochrome c reductase cytochrome b subunit	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity quinol-cytochrome-c reductase activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity cation binding ion binding binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity quinol-cytochrome-c reductase activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity cation binding ion binding binding metal ion binding small molecule binding	cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy	cell periphery cellular anatomical structure plasma membrane membrane
A [auth E], M [auth Q]	Cytochrome c oxidase subunit 2	cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity	aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds respiratory electron transport chain ATP synthesis coupled electron transport electron transport chain metabolic process cellular process generation of precursor metabolites and energy	cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
H [auth Y], T [auth Z]	IPR036423	Superoxide dismutase-like, copper/zinc binding domain superfamily	Homologous Superfamily
H [auth Y], T [auth Z]	IPR018152	Superoxide dismutase, copper/zinc, binding site	Binding Site
H [auth Y], T [auth Z]	IPR001424	Superoxide dismutase, copper/zinc binding domain	Domain
G [auth D], S [auth P]	IPR024341	Protein of unknown function DUF2631	Family
F [auth J], R [auth V]	IPR033437	Protein of unknown function DUF5130	Family
D [auth H], P [auth T]	IPR021050	Cytochrome c oxidase subunit IV, actinobacteria	Family
C [auth G], O [auth S]	IPR035973	Cytochrome c oxidase subunit III-like superfamily	Homologous Superfamily
C [auth G], O [auth S]	IPR013833	Cytochrome c oxidase, subunit III, 4-helical bundle	Homologous Superfamily
C [auth G], O [auth S]	IPR000298	Cytochrome c oxidase subunit III-like	Domain
C [auth G], O [auth S]	IPR024791	Cytochrome c oxidase subunit III	Family
L [auth A], X [auth M]	IPR017941	Rieske [2Fe-2S] iron-sulphur domain	Domain
L [auth A], X [auth M]	IPR045603	QcrA subunit, N-terminal	Domain
L [auth A], X [auth M]	IPR036922	Rieske [2Fe-2S] iron-sulphur domain superfamily	Homologous Superfamily
L [auth A], X [auth M]	IPR014349	Rieske iron-sulphur protein	Family
K [auth C], W [auth O]	IPR009152	Cytochrome bc1 complex, cytochrome c subunit	Family
K [auth C], W [auth O]	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
K [auth C], W [auth O]	IPR050597	Cytochrome c Oxidase Subunit	Family
K [auth C], W [auth O]	IPR009056	Cytochrome c-like domain	Domain
J [auth B], V [auth N]	IPR027387	Cytochrome b/b6-like domain superfamily	Homologous Superfamily
J [auth B], V [auth N]	IPR016174	Di-haem cytochrome, transmembrane	Homologous Superfamily
J [auth B], V [auth N]	IPR005797	Cytochrome b/b6, N-terminal domain	Domain
A [auth E], M [auth Q]	IPR002429	Cytochrome c oxidase subunit II-like C-terminal	Domain
A [auth E], M [auth Q]	IPR036257	Cytochrome C oxidase subunit II, transmembrane domain superfamily	Homologous Superfamily
A [auth E], M [auth Q]	IPR008972	Cupredoxin	Homologous Superfamily
A [auth E], M [auth Q]	IPR001505	Copper centre Cu(A)	Binding Site
A [auth E], M [auth Q]	IPR045187	Cytochrome c/quinol oxidase subunit II	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth E], C [auth G], D [auth H], E [auth I], G [auth D] A [auth E], C [auth G], D [auth H], E [auth I], G [auth D], H [auth Y], I [auth K], J [auth B], K [auth C], L [auth A], M [auth Q], O [auth S], P [auth T], Q [auth U], S [auth P], T [auth Z], U [auth W], V [auth N], W [auth O], X [auth M]	OPM	Transmembrane	Alpha-helical polytopic	Electron transport chain complex IV (cytochrome c oxidase)	Respiratory supercomplexes III-IV

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A [auth E], C [auth G], D [auth H], E [auth I], G [auth D] A [auth E], C [auth G], D [auth H], E [auth I], G [auth D], H [auth Y], I [auth K], J [auth B], K [auth C], L [auth A], M [auth Q], O [auth S], P [auth T], Q [auth U], S [auth P], T [auth Z], U [auth W], V [auth N], W [auth O], X [auth M]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth E], C [auth G], D [auth H], E [auth I], G [auth D] A [auth E], C [auth G], D [auth H], E [auth I], G [auth D], H [auth Y], I [auth K], J [auth B], K [auth C], L [auth A], M [auth Q], O [auth S], P [auth T], Q [auth U], S [auth P], T [auth Z], U [auth W], V [auth N], W [auth O], X [auth M]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Supercomplexes (Respirasome)	Respiratory supercomplex CIII₂CIV₂SOD₂