1FFT

The structure of ubiquinol oxidase from Escherichia coli

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1ffta_	Membrane and cell surface proteins and peptides	Cytochrome c oxidase subunit I-like	Cytochrome c oxidase subunit I-like	Cytochrome c oxidase subunit I-like	Cytochrome O ubiquinol oxidase, subunit I	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E [auth F]	d1fftf_	Membrane and cell surface proteins and peptides	Cytochrome c oxidase subunit I-like	Cytochrome c oxidase subunit I-like	Cytochrome c oxidase subunit I-like	Cytochrome O ubiquinol oxidase, subunit I	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1fftb1	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	d1fftb2	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)
F [auth G]	d1fftg1	All beta proteins	Cupredoxin-like	Cupredoxins	Periplasmic domain of cytochrome c oxidase subunit II	Quinol oxidase (CyoA)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F [auth G]	d1fftg2	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)
C	d1fftc2	Membrane and cell surface proteins and peptides	Cytochrome c oxidase subunit III-like	Cytochrome c oxidase subunit III-like	Cytochrome c oxidase subunit III-like	Cytochrome O ubiquinol oxidase, subunit III	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1fftc3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G [auth H]	d1ffth2	Membrane and cell surface proteins and peptides	Cytochrome c oxidase subunit III-like	Cytochrome c oxidase subunit III-like	Cytochrome c oxidase subunit III-like	Cytochrome O ubiquinol oxidase, subunit III	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G [auth H]	d1ffth3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(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)
A	SCOP2 Family	Cytochrome c oxidase subunit I-like	8025432	4001989	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cytochrome c oxidase subunit I-like	8037811	3000653	SCOP2 (2022-06-29)
E [auth F]	SCOP2B Superfamily	Cytochrome c oxidase subunit I-like	8037811	3000653	SCOP2B (2022-06-29)
B	SCOP2 Family	Cytochrome c oxidase subunit II-like transmembrane region	8025433	4002011	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Cytochrome c oxidase subunit II-like transmembrane region	8037812	3000692	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Cupredoxins	8040569	3000886	SCOP2B (2022-06-29)
F [auth G]	SCOP2B Superfamily	Cupredoxins	8040569	3000886	SCOP2B (2022-06-29)
F [auth G]	SCOP2B Superfamily	Cytochrome c oxidase subunit II-like transmembrane region	8037812	3000692	SCOP2B (2022-06-29)
C	SCOP2 Family	Cytochrome c oxidase subunit III-like	8025435	4002000	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Cytochrome c oxidase subunit III-like	8037814	3000671	SCOP2 (2022-06-29)
G [auth H]	SCOP2B Superfamily	Cytochrome c oxidase subunit III-like	8037814	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	COX1	e1fftA1	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)
E [auth F]	COX1	e1fftF1	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)
B	COX2	e1fftB1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: COX2	ECOD (1.6)
B	COX2_TM_1	e1fftB2	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: COX2_TM_1	ECOD (1.6)
F [auth G]	COX2	e1fftG1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: COX2	ECOD (1.6)
F [auth G]	COX2_TM_1	e1fftG2	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: COX2_TM_1	ECOD (1.6)
C	COX3	e1fftC1	A: alpha bundles	X: Cytochrome c oxidase subunit III-like (From Topology)	H: Cytochrome c oxidase subunit III-like (From Topology)	T: Cytochrome c oxidase subunit III-like	F: COX3	ECOD (1.6)
G [auth H]	COX3	e1fftH1	A: alpha bundles	X: Cytochrome c oxidase subunit III-like (From Topology)	H: Cytochrome c oxidase subunit III-like (From Topology)	T: Cytochrome c oxidase subunit III-like	F: COX3	ECOD (1.6)

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 (4.3.0)
E [auth F]	1.20.210.10	Mainly Alpha	Up-down Bundle	Cytochrome C Oxidase	Chain A	CATH (4.3.0)
B	1.10.287.90	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
B	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.3.0)
F [auth G]	1.10.287.90	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
F [auth G]	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.3.0)
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 (4.3.0)
G [auth H]	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 (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, E [auth F]	PF00115	Cytochrome C and Quinol oxidase polypeptide I (COX1)	Cytochrome C and Quinol oxidase polypeptide I	-	Family
B, F [auth G]	PF00116	Cytochrome C oxidase subunit II, periplasmic domain (COX2)	Cytochrome C oxidase subunit II, periplasmic domain	-	Domain
B, F [auth G]	PF06481	COX Aromatic Rich Motif (COX_ARM)	COX Aromatic Rich Motif	-	Motif
C, G [auth H]	PF00510	Cytochrome c oxidase subunit III (COX3)	Cytochrome c oxidase subunit III	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, E [auth F]	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 oxidoreductase activity inorganic molecular entity transmembrane transporter activity oxidoreductase activity, acting on a heme group of donors inorganic cation transmembrane transporter activity 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 oxidoreductase activity inorganic molecular entity transmembrane transporter activity oxidoreductase activity, acting on a heme group of donors inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity catalytic activity binding organic cyclic compound 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, acting on diphenols and related substances as donors cytochrome bo3 ubiquinol oxidase activity	electron transport coupled proton transport transport proton transmembrane transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization energy coupled proton transmembrane transport, against electrochemical gradient monoatomic ion transport cellular process monoatomic cation transport electron transport coupled proton transport transport proton transmembrane transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport transmembrane transport monoatomic cation 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 cellular metabolic process metabolic process generation of precursor metabolites and energy aerobic electron transport chain oxidative phosphorylation electron transport chain respiratory electron transport chain	membrane respirasome cellular anatomical entity protein-containing complex catalytic complex cytochrome complex transmembrane transporter complex cytochrome o ubiquinol oxidase complex membrane protein complex oxidoreductase complex transporter complex cell periphery plasma membrane
B, F [auth G]	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 oxidoreductase activity inorganic molecular entity transmembrane transporter activity oxidoreductase activity, acting on a heme group of donors inorganic cation transmembrane transporter activity 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 oxidoreductase activity inorganic molecular entity transmembrane transporter activity oxidoreductase activity, acting on a heme group of donors inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity catalytic 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, acting on diphenols and related substances as donors cytochrome bo3 ubiquinol oxidase activity	electron transport coupled proton transport transport proton transmembrane transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization energy coupled proton transmembrane transport, against electrochemical gradient monoatomic ion transport cellular process monoatomic cation transport electron transport coupled proton transport transport proton transmembrane transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport transmembrane transport monoatomic cation 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 cellular metabolic process metabolic process generation of precursor metabolites and energy aerobic electron transport chain oxidative phosphorylation electron transport chain respiratory electron transport chain ATP synthesis coupled electron transport	membrane respirasome cellular anatomical entity protein-containing complex catalytic complex cytochrome complex transmembrane transporter complex cytochrome o ubiquinol oxidase complex membrane protein complex oxidoreductase complex transporter complex cell periphery plasma membrane
C, G [auth H]	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 oxidoreductase activity inorganic molecular entity transmembrane transporter activity oxidoreductase activity, acting on a heme group of donors inorganic cation transmembrane transporter activity 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 oxidoreductase activity inorganic molecular entity transmembrane transporter activity oxidoreductase activity, acting on a heme group of donors inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity catalytic activity cytochrome bo3 ubiquinol oxidase activity	electron transport coupled proton transport transport proton transmembrane transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization energy coupled proton transmembrane transport, against electrochemical gradient monoatomic ion transport cellular process monoatomic cation transport electron transport coupled proton transport transport proton transmembrane transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport transmembrane transport monoatomic cation 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 cellular metabolic process metabolic process generation of precursor metabolites and energy aerobic electron transport chain oxidative phosphorylation electron transport chain respiratory electron transport chain	protein-containing complex catalytic complex cytochrome complex transmembrane transporter complex cytochrome o ubiquinol oxidase complex membrane membrane protein complex oxidoreductase complex cellular anatomical entity transporter complex cell periphery plasma membrane
D, H [auth I]	UBIQUINOL OXIDASE	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Membrane Protein Annotation: OPM OPM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, E [auth F], F [auth G] A, B, C, E [auth F], F [auth G], G [auth H]	MemProtMD	Annotated as membrane protein by MemProtMD

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	ubiquinol oxidase (H+-transporting) M-CSA #714	The cytochrome bo3 ubiquinol oxidase from E. coli is a terminal enzyme in the respiratory chain, oxidising the membrane-soluble ubiquinol-8 and reducing molecular dioxygen, and pumping four protons across the membrane to generate a proton gradient that is used to drive ATP synthesis. Ubiquinol oxidase is homologous to cytochrome c oxidase; both have four subunits, the same redox mechanism, the same electron transfer pathway and conserved proton pumping channels.	Defined by 23 residues: TYR:A-61ARG:A-71ASP:A-75MET:A-79PHE:A-103ASN:A-124ASP:A-135ASN:A-142SER:A-145THR:A-149THR:A-201THR:A-204THR:A-211HIS:A-284GLU:A-286TYR:A-288SER:A-299SER:A-315THR:A-359LYS:A-362HIS:A-419PHE:A-420HIS:A-421 \| Explore in 3D: M-CSA Motif Definition Up to 10 residues are supported for Structure Motif searching, this motif has 23 residues. EC: 1.10.3 (PDB Primary Data)

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.