3MK7 | pdb_00003mk7

The structure of CBB3 cytochrome oxidase

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
L [auth M]	F5_F8_type_C	e3mk7M1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: F5_F8_type_C	ECOD (v294.1)
I	F5_F8_type_C	e3mk7I1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: F5_F8_type_C	ECOD (v294.1)
F	Cytochrome_CBB3	e3mk7F1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Cytochrome_CBB3	ECOD (v294.1)
F	F5_F8_type_C	e3mk7F3	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: F5_F8_type_C	ECOD (v294.1)
C	CBS	e3mk7C1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: CBS	ECOD (v294.1)
K [auth L]	Cytochrome_CBB3	e3mk7L1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Cytochrome_CBB3	ECOD (v294.1)
H	Cytochrome_CBB3	e3mk7H1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Cytochrome_CBB3	ECOD (v294.1)
E	Cytochrome_CBB3	e3mk7E1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Cytochrome_CBB3	ECOD (v294.1)
B	FixO	e3mk7B1	A: a/b three-layered sandwiches	X: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains	H: N-terminal domain in beta subunit of DNA dependent RNA-polymerase	T: N-terminal domain in beta subunit of DNA dependent RNA-polymerase	F: FixO	ECOD (v294.1)
J [auth K]	Cytochrome_CBB3	e3mk7K1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Cytochrome_CBB3	ECOD (v294.1)
G	Cytochrome_CBB3	e3mk7G1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Cytochrome_CBB3	ECOD (v294.1)
D	Cytochrome_CBB3	e3mk7D1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Cytochrome_CBB3	ECOD (v294.1)
A	FtsJ	e3mk7A1	A: a/b three-layered sandwiches	X: Ribonuclease H-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: FtsJ	ECOD (v294.1)

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)
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)
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)
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)
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)
A	1.20.210.10	Mainly Alpha	Up-down Bundle	Cytochrome C Oxidase	Chain A	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
M [auth U], N [auth X], O [auth Y], P [auth Z]	30-mer peptide	-	-	-
C, F, I, L [auth M]	Cytochrome c oxidase, cbb3-type, subunit P	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]	Cytochrome c oxidase, cbb3-type, subunit O	binding tetrapyrrole binding heme binding electron transfer activity cation binding ion binding metal ion binding small molecule binding	-	protein-containing complex cytochrome complex catalytic complex
A, D, G, J [auth K]	Cytochrome c oxidase, cbb3-type, subunit N	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

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J [auth K], K [auth L], L [auth M]	OPM	Transmembrane	Alpha-helical polytopic	Electron transport chain complex IV (cytochrome c oxidase)	Cytochrome c oxidases

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F, G, H, I, J [auth K], K [auth L], L [auth M]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F, G, H, I, J [auth K], K [auth L], L [auth M]	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D, E A, B, C, D, E, F, G, H, I, J [auth K], K [auth L], L [auth M]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)	Cytochrome Oxidase, cbb₃