6KOB | pdb_00006kob

X-ray Structure of the proton-pumping cytochrome aa3-600 menaquinol oxidase from Bacillus subtilis

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: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Cytochrome c oxidase subunit I-like	8098640	3000653	SCOP2B (2022-06-29)
H [auth E]	SCOP2 Family	Cytochrome c oxidase subunit I-like	8098639	4001989	SCOP2 (2022-06-29)
H [auth E]	SCOP2 Superfamily	Cytochrome c oxidase subunit I-like	8098640	3000653	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Cytochrome c oxidase subunit III-like	8095433	3000671	SCOP2B (2022-06-29)
E [auth G]	SCOP2B Superfamily	Cytochrome c oxidase subunit III-like	8095433	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)
A		e6kobA1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F:	ECOD (develop294)
H [auth E]		e6kobE1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F:	ECOD (develop294)
B	bZIP_1	e6kobB1	A: alpha bundles	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: bZIP_1	ECOD (develop294)
G [auth F]	bZIP_1	e6kobF1	A: alpha bundles	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: bZIP_1	ECOD (develop294)
C	bZIP_1	e6kobC1	A: alpha bundles	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: bZIP_1	ECOD (develop294)
E [auth G]	bZIP_1	e6kobG1	A: alpha bundles	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: bZIP_1	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.210.10	Mainly Alpha	Up-down Bundle	Cytochrome C Oxidase	Chain A	CATH (utative)
H [auth E]	1.20.210.10	Mainly Alpha	Up-down Bundle	Cytochrome C Oxidase	Chain A	CATH (utative)
B	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (utative)
G [auth F]	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (utative)
C	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)
E [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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, H [auth E]	PF00115	Cytochrome C and Quinol oxidase polypeptide I (COX1)	Cytochrome C and Quinol oxidase polypeptide I	-	Family
B, G [auth F]	PF00116	Cytochrome C oxidase subunit II, periplasmic domain (COX2)	Cytochrome C oxidase subunit II, periplasmic domain		Domain
D, F [auth H]	PF03626	Prokaryotic Cytochrome C oxidase subunit IV (COX4_pro)	Prokaryotic Cytochrome C oxidase subunit IV	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, H [auth E]	AA3-600 quinol oxidase subunit I	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 binding tetrapyrrole binding heme 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 binding tetrapyrrole binding heme binding cation binding transition metal ion binding copper ion binding ion binding metal ion binding small molecule binding oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor oxidoreductase activity oxidoreductase activity, acting on diphenols and related substances as donors catalytic activity	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 aerobic respiration cellular respiration 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 aerobic respiration cellular respiration energy derivation by oxidation of organic compounds metabolic process generation of precursor metabolites and energy oxidative phosphorylation respiratory electron transport chain ATP synthesis coupled electron transport electron transport chain	cell periphery cellular anatomical structure plasma membrane membrane
B, G [auth F]	Quinol oxidase subunit 2	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 cation binding transition metal ion binding copper ion 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 cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor oxidoreductase activity oxidoreductase activity, acting on diphenols and related substances as donors catalytic activity cytochrome bo3 ubiquinol oxidase activity oxidoreductase activity, acting on a heme group of donors	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	cell periphery cellular anatomical structure plasma membrane membrane membrane microdomain membrane raft respiratory chain complex protein-containing complex
D, F [auth H]	AA3-600 quinol oxidase subunit IV,Quinol oxidase subunit 4	oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor oxidoreductase activity oxidoreductase activity, acting on diphenols and related substances as donors catalytic activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity electron transfer activity cytochrome bo3 ubiquinol oxidase activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity primary active transmembrane transporter activity oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor oxidoreductase activity oxidoreductase activity, acting on diphenols and related substances as donors catalytic activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity electron transfer activity cytochrome bo3 ubiquinol oxidase activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity primary active transmembrane transporter activity oxidoreductase activity, acting on a heme group of donors	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 ATP synthesis coupled electron transport electron transport coupled proton transport transport proton transmembrane transport 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 ATP synthesis coupled electron transport 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 monoatomic cation transport	respiratory chain complex protein-containing complex catalytic complex cytochrome complex membrane membrane protein complex transporter complex cellular anatomical structure transmembrane transporter complex cytochrome o ubiquinol oxidase complex oxidoreductase complex cell periphery plasma membrane
C, E [auth G]	AA3-600 quinol oxidase subunit IIII	oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor oxidoreductase activity oxidoreductase activity, acting on diphenols and related substances as donors 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 monoatomic ion transmembrane transporter activity transporter activity oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor oxidoreductase activity oxidoreductase activity, acting on diphenols and related substances as donors 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 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 ATP synthesis coupled electron transport	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, H [auth E]	IPR036927	Cytochrome c oxidase-like, subunit I superfamily	Homologous Superfamily
A, H [auth E]	IPR000883	Cytochrome c oxidase subunit I	Family
A, H [auth E]	IPR023615	Cytochrome c oxidase, subunit I, copper-binding site	Binding Site
A, H [auth E]	IPR023616	Cytochrome c oxidase-like, subunit I domain	Domain
A, H [auth E]	IPR014233	Quinol oxidase subunit I	Family
B, G [auth F]	IPR006333	Cytochrome o ubiquinol oxidase subunit II	Family
B, G [auth F]	IPR011759	Cytochrome C oxidase subunit II, transmembrane domain	Domain
B, G [auth F]	IPR036257	Cytochrome C oxidase subunit II, transmembrane domain superfamily	Homologous Superfamily
B, G [auth F]	IPR045187	Cytochrome c/quinol oxidase subunit II	Family
B, G [auth F]	IPR034227	Ubiquinol oxidase subunit 2, cupredoxin domain	Domain
B, G [auth F]	IPR002429	Cytochrome c oxidase subunit II-like C-terminal	Domain
B, G [auth F]	IPR008972	Cupredoxin	Homologous Superfamily
B, G [auth F]	IPR006332	Quinol oxidase subunit II	Family
D, F [auth H]	IPR050968	Cytochrome c oxidase bacterial subunit 4	Family
D, F [auth H]	IPR014250	Quinol oxidase subunit IV	Family
D, F [auth H]	IPR005171	Cytochrome C oxidase subunit IV, prokaryotes	Family
C, E [auth G]	IPR035973	Cytochrome c oxidase subunit III-like superfamily	Homologous Superfamily
C, E [auth G]	IPR013833	Cytochrome c oxidase, subunit III, 4-helical bundle	Homologous Superfamily
C, E [auth G]	IPR000298	Cytochrome c oxidase subunit III-like	Domain
C, E [auth G]	IPR024791	Cytochrome c oxidase subunit III	Family
C, E [auth G]	IPR014246	Quinol oxidase subunit III	Family
C, E [auth G]	IPR033946	Ubiquinol oxidase subunit III domain	Domain

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D, E [auth G] A, B, C, D, E [auth G], F [auth H], G [auth F], H [auth E]	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 [auth G] A, B, C, D, E [auth G], F [auth H], G [auth F], H [auth E]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D, E [auth G] A, B, C, D, E [auth G], F [auth H], G [auth F], H [auth E]	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 [auth G] A, B, C, D, E [auth G], F [auth H], G [auth F], H [auth E]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)	cytochrome aa₃-600 menaquinol oxidase