9GY6 | pdb_00009gy6

Mycobacterial cytochrome bc1:aa3 with inhibitor

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
R [auth S]	SCOP2B Superfamily	Cytochrome c oxidase subunit III-like	8075786	3000671	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Cytochrome c oxidase subunit III-like	8075786	3000671	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)
R [auth S]	Beta-Casp	e9gy6S1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
G	Beta-Casp	e9gy6G1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
Q [auth R]	Beta-Casp	e9gy6R1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
F	Beta-Casp	e9gy6F1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
P [auth Q]	Beta-Casp	e9gy6Q1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
E	Beta-Casp	e9gy6E1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
N [auth O]	Beta-Casp	e9gy6O1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
C	Beta-Casp	e9gy6C1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
M [auth N]	Beta-Casp	e9gy6N1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
B	V-set	e9gy6B01	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: V-set	ECOD (v294.2)
V [auth X]	Beta-Casp	e9gy6X1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
K [auth L]	Beta-Casp	e9gy6L1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
U [auth V]	Beta-Casp	e9gy6V1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
J	Beta-Casp	e9gy6J1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
H, S [auth T]	PF12270	Cytochrome c oxidase subunit IV (Cyt_c_ox_IV)	Cytochrome c oxidase subunit IV	-	Family
C, N [auth O]	PF13442	Cytochrome C oxidase, cbb3-type, subunit III (Cytochrome_CBB3)	Cytochrome C oxidase, cbb3-type, subunit III		Domain
C, N [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
B, M [auth N]	PF13631	Cytochrome b(N-terminal)/b6/petB (Cytochrom_B_N_2)	Cytochrome b(N-terminal)/b6/petB		Domain
J, U [auth V]	PF17174	Domain of unknown function (DUF5130) (DUF5130)	Domain of unknown function (DUF5130)	-	Family
A, L [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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I, T [auth U]	Secreted protein	-	-	-
H, S [auth T]	Cytochrome c oxidase polypeptide 4	oxidoreductase activity catalytic activity 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 oxidoreductase activity, acting on a heme group of donors 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
G, R [auth S]	Cytochrome c oxidase subunit 3	oxidoreductase activity catalytic activity 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 oxidoreductase activity, acting on a heme group of donors 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
F, Q [auth R]	Cytochrome c oxidase subunit 1	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 oxidoreductase activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity oxidoreductase activity, acting on a heme group of donors monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity catalytic activity 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 oxidoreductase activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity oxidoreductase activity, acting on a heme group of donors monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity catalytic activity binding tetrapyrrole binding heme binding cation binding ion binding metal ion binding small molecule binding	electron transport coupled proton transport transport proton transmembrane transport monoatomic ion transmembrane transport establishment of localization monoatomic cation transmembrane transport transmembrane transport localization energy coupled proton transmembrane transport, against electrochemical gradient monoatomic ion transport cellular process monoatomic cation transport cellular respiration energy derivation by oxidation of organic compounds electron transport coupled proton transport transport proton transmembrane transport monoatomic ion transmembrane transport establishment of localization monoatomic cation transmembrane transport transmembrane transport localization energy coupled proton transmembrane transport, against electrochemical gradient monoatomic ion transport cellular process monoatomic cation transport cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process generation of precursor metabolites and energy aerobic respiration oxidative phosphorylation	cell periphery cellular anatomical structure plasma membrane membrane
E, P [auth Q]	Cytochrome c oxidase subunit 2	oxidoreductase activity catalytic 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 oxidoreductase activity catalytic 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 oxidoreductase activity, acting on a heme group of donors 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
D, O [auth P]	Transmembrane protein	-	-	-
C, N [auth O]	Cytochrome bc1 complex cytochrome c subunit	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity oxidoreductase activity, acting on diphenols and related substances as donors primary active transmembrane transporter activity oxidoreductase 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 catalytic activity transmembrane transporter activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity oxidoreductase activity, acting on diphenols and related substances as donors primary active transmembrane transporter activity oxidoreductase 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 catalytic 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
B, M [auth N]	Cytochrome bc1 complex cytochrome b subunit	oxidoreductase activity catalytic activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity oxidoreductase activity, acting on diphenols and related substances as donors 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 oxidoreductase activity catalytic activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity oxidoreductase activity, acting on diphenols and related substances as donors 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
K [auth L], V [auth X]	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	-	-
J, U [auth V]	DUF5130 domain-containing protein	-	-	-
A, L [auth M]	Cytochrome bc1 complex Rieske iron-sulfur subunit	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
H, S [auth T]	IPR021050	Cytochrome c oxidase subunit IV, actinobacteria	Family
G, R [auth S]	IPR035973	Cytochrome c oxidase subunit III-like superfamily	Homologous Superfamily
G, R [auth S]	IPR013833	Cytochrome c oxidase, subunit III, 4-helical bundle	Homologous Superfamily
G, R [auth S]	IPR000298	Cytochrome c oxidase subunit III-like	Domain
G, R [auth S]	IPR024791	Cytochrome c oxidase subunit III	Family
F, Q [auth R]	IPR036927	Cytochrome c oxidase-like, subunit I superfamily	Homologous Superfamily
F, Q [auth R]	IPR000883	Cytochrome c oxidase subunit I	Family
F, Q [auth R]	IPR023615	Cytochrome c oxidase, subunit I, copper-binding site	Binding Site
F, Q [auth R]	IPR023616	Cytochrome c oxidase-like, subunit I domain	Domain
F, Q [auth R]	IPR014241	Cytochrome c oxidase, subunit I bacterial type	Family
E, P [auth Q]	IPR002429	Cytochrome c oxidase subunit II-like C-terminal	Domain
E, P [auth Q]	IPR036257	Cytochrome C oxidase subunit II, transmembrane domain superfamily	Homologous Superfamily
E, P [auth Q]	IPR008972	Cupredoxin	Homologous Superfamily
E, P [auth Q]	IPR001505	Copper centre Cu(A)	Binding Site
E, P [auth Q]	IPR045187	Cytochrome c/quinol oxidase subunit II	Family
D, O [auth P]	IPR024341	Protein of unknown function DUF2631	Family
C, N [auth O]	IPR009152	Cytochrome bc1 complex, cytochrome c subunit	Family
C, N [auth O]	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
C, N [auth O]	IPR050597	Cytochrome c Oxidase Subunit	Family
C, N [auth O]	IPR009056	Cytochrome c-like domain	Domain
B, M [auth N]	IPR027387	Cytochrome b/b6-like domain superfamily	Homologous Superfamily
B, M [auth N]	IPR016174	Di-haem cytochrome, transmembrane	Homologous Superfamily
B, M [auth N]	IPR005797	Cytochrome b/b6, N-terminal domain	Domain
K [auth L], V [auth X]	IPR036423	Superoxide dismutase-like, copper/zinc binding domain superfamily	Homologous Superfamily
K [auth L], V [auth X]	IPR018152	Superoxide dismutase, copper/zinc, binding site	Binding Site
K [auth L], V [auth X]	IPR001424	Superoxide dismutase, copper/zinc binding domain	Domain
J, U [auth V]	IPR033437	Protein of unknown function DUF5130	Family
A, L [auth M]	IPR017941	Rieske [2Fe-2S] iron-sulphur domain	Domain
A, L [auth M]	IPR045603	QcrA subunit, N-terminal	Domain
A, L [auth M]	IPR036922	Rieske [2Fe-2S] iron-sulphur domain superfamily	Homologous Superfamily
A, L [auth M]	IPR014349	Rieske iron-sulphur protein	Family

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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.