6WTI | pdb_00006wti

The Cryo-EM structure of the ubiquinol oxidase from Escherichia coli

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d6wtib2	All beta proteins	Cupredoxin-like	Cupredoxins	Periplasmic domain of cytochrome c oxidase subunit II	Quinol oxidase (CyoA)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d6wtib1	Membrane and cell surface proteins and peptides	Transmembrane helix hairpin	Cytochrome c oxidase subunit II-like, transmembrane region	Cytochrome c oxidase subunit II-like, transmembrane region	Cytochrome O ubiquinol oxidase, subunit II	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Cytochrome c oxidase subunit III-like	8037814	3000671	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cytochrome c oxidase subunit II-like, transmembrane region	8037812	3000692	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cupredoxins	8040569	3000886	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cytochrome c oxidase subunit I-like	8037811	3000653	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)
C	GFP	e6wtiC1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F: GFP	ECOD (v294.1)
B	GFP	e6wtiB1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F: GFP	ECOD (v294.1)
A	GFP	e6wtiA1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F: GFP	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D	PF03626	Prokaryotic Cytochrome C oxidase subunit IV (COX4_pro)	Prokaryotic Cytochrome C oxidase subunit IV	-	Family
B	PF00116	Cytochrome C oxidase subunit II, periplasmic domain (COX2)	Cytochrome C oxidase subunit II, periplasmic domain		Domain
B	PF06481	COX Aromatic Rich Motif (COX_ARM)	COX Aromatic Rich Motif	-	Motif
A	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
D	Cytochrome o ubiquinol oxidase, subunit IV	oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity primary active transmembrane transporter activity transporter activity transmembrane transporter activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity monoatomic ion transmembrane transporter activity electron transfer activity oxidoreductase activity cytochrome bo3 ubiquinol oxidase activity oxidoreductase activity, acting on a heme group of donors catalytic 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 electron transport coupled proton transport transport proton transmembrane transport monoatomic ion 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 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	Cytochrome o ubiquinol oxidase	oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity primary active transmembrane transporter activity transporter activity transmembrane transporter activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity monoatomic ion transmembrane transporter activity oxidoreductase activity cytochrome bo3 ubiquinol oxidase activity oxidoreductase activity, acting on a heme group of donors oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity primary active transmembrane transporter activity transporter activity transmembrane transporter activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity monoatomic ion transmembrane transporter activity oxidoreductase activity cytochrome bo3 ubiquinol oxidase activity oxidoreductase activity, acting on a heme group of 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 aerobic electron transport chain oxidative phosphorylation respiratory electron transport chain electron transport chain	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
B	Ubiquinol oxidase subunit 2	oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity primary active transmembrane transporter activity transporter activity transmembrane transporter activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity monoatomic ion transmembrane transporter activity cation binding transition metal ion binding copper ion binding oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity primary active transmembrane transporter activity transporter activity transmembrane transporter activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity monoatomic ion 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	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 aerobic electron transport chain oxidative phosphorylation respiratory electron transport chain electron transport chain ATP synthesis coupled electron 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
A	Cytochrome o ubiquinol oxidase, subunit I	oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity primary active transmembrane transporter activity transporter activity transmembrane transporter activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity monoatomic ion transmembrane transporter activity binding tetrapyrrole binding heme binding oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity primary active transmembrane transporter activity transporter activity transmembrane transporter activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity monoatomic ion transmembrane transporter activity binding tetrapyrrole binding heme binding quinone binding ubiquinone binding small molecule binding cation binding transition metal ion binding copper ion binding ion binding metal ion 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	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 aerobic electron transport chain oxidative phosphorylation respiratory electron transport chain electron transport chain	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D	IPR014210	Cytochrome o ubiquinol oxidase subunit IV	Family
D	IPR050968	Cytochrome c oxidase bacterial subunit 4	Family
D	IPR005171	Cytochrome C oxidase subunit IV, prokaryotes	Family
C	IPR035973	Cytochrome c oxidase subunit III-like superfamily	Homologous Superfamily
C	IPR000298	Cytochrome c oxidase subunit III-like	Domain
C	IPR013833	Cytochrome c oxidase, subunit III, 4-helical bundle	Homologous Superfamily
C	IPR014206	Cytochrome o ubiquinol oxidase, subunit III	Family
C	IPR024791	Cytochrome c oxidase subunit III	Family
C	IPR033946	Ubiquinol oxidase subunit III domain	Domain
B	IPR006333	Cytochrome o ubiquinol oxidase subunit II	Family
B	IPR011759	Cytochrome C oxidase subunit II, transmembrane domain	Domain
B	IPR036257	Cytochrome C oxidase subunit II, transmembrane domain superfamily	Homologous Superfamily
B	IPR045187	Cytochrome c/quinol oxidase subunit II	Family
B	IPR034227	Ubiquinol oxidase subunit 2, cupredoxin domain	Domain
B	IPR002429	Cytochrome c oxidase subunit II-like C-terminal	Domain
B	IPR008972	Cupredoxin	Homologous Superfamily
B	IPR010514	COX aromatic rich motif	Domain
A	IPR036927	Cytochrome c oxidase-like, subunit I superfamily	Homologous Superfamily
A	IPR000883	Cytochrome c oxidase subunit I	Family
A	IPR023615	Cytochrome c oxidase, subunit I, copper-binding site	Binding Site
A	IPR023616	Cytochrome c oxidase-like, subunit I domain	Domain
A	IPR014207	Cytochrome o ubiquinol oxidase, subunit I	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D	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	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)	Ubiquinol Oxidase, cytochrome bo₃