5DJQ | pdb_00005djq

The structure of CBB3 cytochrome oxidase.

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
L [auth M]	Cytochrome_CBB3	e5djqM1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Cytochrome_CBB3	ECOD (1.6)
L [auth M]	FixP_N	e5djqM3	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: FixP_N	ECOD (1.6)
I	Cytochrome_CBB3	e5djqI2	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Cytochrome_CBB3	ECOD (1.6)
I	FixP_N	e5djqI1	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: FixP_N	ECOD (1.6)
F	Cytochrome_CBB3	e5djqF1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Cytochrome_CBB3	ECOD (1.6)
F	FixP_N	e5djqF3	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: FixP_N	ECOD (1.6)
C	Cytochrome_CBB3	e5djqC3	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Cytochrome_CBB3	ECOD (1.6)
C	FixP_N	e5djqC1	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: FixP_N	ECOD (1.6)
H	FixO	e5djqH1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: FixO	ECOD (1.6)
K [auth L]	FixO	e5djqL1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: FixO	ECOD (1.6)
E	FixO	e5djqE1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: FixO	ECOD (1.6)
B	FixO	e5djqB1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: FixO	ECOD (1.6)
A	COX1	e5djqA1	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)
J [auth K]	COX1	e5djqK1	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)
G	COX1	e5djqG1	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)
D	COX1	e5djqD1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L [auth M]	6.10.280.130	Special	Helix non-globular	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
L [auth M]	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
I	6.10.280.130	Special	Helix non-globular	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
I	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
F	6.10.280.130	Special	Helix non-globular	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
F	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
C	6.10.280.130	Special	Helix non-globular	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
C	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
H	6.10.250.2250	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
H	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
K [auth L]	6.10.250.2250	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
K [auth L]	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
E	6.10.250.2250	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
E	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
B	6.10.250.2250	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
A	1.20.210.10	Mainly Alpha	Up-down Bundle	Cytochrome C Oxidase	Chain A	CATH (4.3.0)
J [auth K]	1.20.210.10	Mainly Alpha	Up-down Bundle	Cytochrome C Oxidase	Chain A	CATH (4.3.0)
G	1.20.210.10	Mainly Alpha	Up-down Bundle	Cytochrome C Oxidase	Chain A	CATH (4.3.0)
D	1.20.210.10	Mainly Alpha	Up-down Bundle	Cytochrome C Oxidase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F, I, L [auth M]	PF14715	N-terminal domain of cytochrome oxidase-cbb3, FixP (FixP_N)	N-terminal domain of cytochrome oxidase-cbb3, FixP	This is the N-terminal domain of FixP, the cytochrome oxidase type-cbb3. the exact function is not known.	Domain
C, F, I, L [auth M]	PF13442	Cytochrome C oxidase, cbb3-type, subunit III (Cytochrome_CBB3)	Cytochrome C oxidase, cbb3-type, subunit III		Domain
A, D, G, J [auth K]	PF00115	Cytochrome C and Quinol oxidase polypeptide I (COX1)	Cytochrome C and Quinol oxidase polypeptide I	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
M [auth N], N [auth O], O [auth P], P [auth Q]	Putative uncharacterized protein	-	-	-
C, F, I, L [auth M]	Cbb3-type cytochrome c oxidase subunit CcoP1	oxidoreductase activity catalytic activity binding tetrapyrrole binding heme binding electron transfer activity cation binding ion binding metal ion binding small molecule binding	monoatomic cation transmembrane transport transmembrane transport localization transport proton transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport cellular process monoatomic cation transport establishment of localization aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds monoatomic cation transmembrane transport transmembrane transport localization transport proton transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport cellular process monoatomic cation transport establishment of localization aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds metabolic process generation of precursor metabolites and energy	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex cytochrome complex catalytic complex
B, E, H, K [auth L]	Cbb3-type cytochrome c oxidase subunit II	binding tetrapyrrole binding heme binding electron transfer activity cation binding ion binding metal ion binding small molecule binding	-	cellular anatomical structure membrane protein-containing complex cytochrome complex catalytic complex
A, D, G, J [auth K]	Cbb3-type cytochrome c oxidase subunit CcoN1	oxygen binding 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 oxygen binding 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 quinol-cytochrome-c reductase activity tetrapyrrole binding heme binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen catalytic activity copper ion binding	monoatomic cation transmembrane transport transmembrane transport localization transport proton transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport cellular process monoatomic cation transport establishment of localization electron transport coupled proton transport energy coupled proton transmembrane transport, against electrochemical gradient aerobic respiration cellular respiration monoatomic cation transmembrane transport transmembrane transport localization transport proton transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport cellular process monoatomic cation transport establishment of localization electron transport coupled proton transport energy coupled proton transmembrane transport, against electrochemical gradient aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds metabolic process generation of precursor metabolites and energy aerobic electron transport chain respiratory electron transport chain electron transport chain energy derivation by oxidation of reduced inorganic compounds aerobic respiration, using ferrous ions as electron donor	cell periphery cellular anatomical structure plasma membrane membrane respiratory chain complex protein-containing complex cytochrome complex catalytic complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F, I, L [auth M]	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
C, F, I, L [auth M]	IPR009056	Cytochrome c-like domain	Domain
C, F, I, L [auth M]	IPR032858	Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal	Domain
C, F, I, L [auth M]	IPR004678	Cytochrome c oxidase cbb3-type, subunit III	Family
C, F, I, L [auth M]	IPR050597	Cytochrome c Oxidase Subunit	Family
C, F, I, L [auth M]	IPR038414	Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal domain superfamily	Homologous Superfamily
B, E, H, K [auth L]	IPR003468	Cytochrome c oxidase, monohaem subunit/FixO	Family
B, E, H, K [auth L]	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
B, E, H, K [auth L]	IPR009056	Cytochrome c-like domain	Domain
A, D, G, J [auth K]	IPR036927	Cytochrome c oxidase-like, subunit I superfamily	Homologous Superfamily
A, D, G, J [auth K]	IPR000883	Cytochrome c oxidase subunit I	Family
A, D, G, J [auth K]	IPR004677	Cytochrome c oxidase cbb3-type, subunit I	Family
A, D, G, J [auth K]	IPR023615	Cytochrome c oxidase, subunit I, copper-binding site	Binding Site
A, D, G, J [auth K]	IPR023616	Cytochrome c oxidase-like, subunit I domain	Domain