1fft

The structure of ubiquinol oxidase from Escherichia coli

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

UBIQUINOL OXIDASE

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	UBIQUINOL OXIDASE × 1 （P0ABJ1） UBIQUINOL OXIDASE × 1 （P0ABJ3） UBIQUINOL OXIDASE × 1 COPPER (II) ION × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 HEME O × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	UBIQUINOL OXIDASE × 1 （P0ABJ1） UBIQUINOL OXIDASE × 1 （P0ABJ3） UBIQUINOL OXIDASE × 1 COPPER (II) ION × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 HEME O × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYOB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–663； UniProt 1–663 Author chain F； PDBConstruct 1–663； UniProt 1–663

UBIQUINOL OXIDASE

Escherichia coli

UniProt P0ABJ1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	UBIQUINOL OXIDASE × 1 （P0ABI8） UBIQUINOL OXIDASE × 1 （P0ABJ3） UBIQUINOL OXIDASE × 1 COPPER (II) ION × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 HEME O × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	UBIQUINOL OXIDASE × 1 （P0ABI8） UBIQUINOL OXIDASE × 1 （P0ABJ3） UBIQUINOL OXIDASE × 1 COPPER (II) ION × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 HEME O × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYOA_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–315； UniProt 1–315 Author chain G； PDBConstruct 1–315； UniProt 1–315

UBIQUINOL OXIDASE

Escherichia coli

UniProt P0ABJ3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	UBIQUINOL OXIDASE × 1 （P0ABI8） UBIQUINOL OXIDASE × 1 （P0ABJ1） UBIQUINOL OXIDASE × 1 COPPER (II) ION × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 HEME O × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	UBIQUINOL OXIDASE × 1 （P0ABI8） UBIQUINOL OXIDASE × 1 （P0ABJ1） UBIQUINOL OXIDASE × 1 COPPER (II) ION × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 HEME O × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYOC_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 25–204； UniProt 25–204 Author chain H； PDBConstruct 25–204； UniProt 25–204

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1fft
Deposition date deposition_date	2000-07-26
Structure title title	The structure of ubiquinol oxidase from Escherichia coli
Keywords keywords	ELECTRON TRANSPORT, CYTOCHROME OXIDASE, MEMBRANE PROTEIN, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1fft__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1fft__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1fft__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	32.13 Å
Rg (electron density)	30.86 Å
Total Rg	31.58 Å
Atom count	8068
Residues	1052
Excluded volume	146100 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1fft__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1fft__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	UBIQUINOL OXIDASE
Molecular weight formula_weight	74424.5 kDa
EC 编号 ec_number	1.10.3.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,F
Atom count atom_count	16136

MFGKLSLDAVPFHEPIVMVTIAGIILGGLALVGLITYFGKWTYLWKEWLTSVDHKRLGIMYIIVAIVMLLRGFADAIMMRSQQALASAGEAGFLPPHHYDQIFTAHGVIMIFFVAMPFVIGLMNLVVPLQIGARDVAFPFLNNLSFWFTVVGVILVNVSLGVGEFAQTGWLAYPPLSGIEYSPGVGVDYWIWSLQLSGIGTTLTGINFFVTILKMRAPGMTMFKMPVFTWASLCANVLIIASFPILTVTVALLTLDRYLGTHFFTNDMGGNMMMYINLIWAWGHPEVYILILPVFGVFSEIAATFSRKRLFGYTSLVWATVCITVLSFIVWLHHFFTMGAGANVNAFFGITTMIIAIPTGVKIFNWLFTMYQGRIVFHSAMLWTIGFIVTFSVGGMTGVLLAVPGADFVLHNSLFLIAHFHNVIIGGVVFGCFAGMTYWWPKAFGFKLNETWGKRAFWFWIIGFFVAFMPLYALGFMGMTRRLSQQIDPQFHTMLMIAASGAVLIALGILCLVIQMYVSIRDRDQNRDLTGDPWGGRTLEWATSSPPPFYNFAVVPHVHERDAFWEMKEKGEAYKKPDHYEEIHMPKNSGAGIVIAAFSTIFGFAMIWHIWWLAIVGFAGMIITWIVKSFDEDVDYYVPVAEIEKLENQHFDEITKAGLKNGN

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	UBIQUINOL OXIDASE
Molecular weight formula_weight	34947.2 kDa
EC 编号 ec_number	1.10.3.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,G

MRLRKYNKSLGWLSLFAGTVLLSGCNSALLDPKGQIGLEQRSLILTAFGLMLIVVIPAILMAVGFAWKYRASNKDAKYSPNWSHSNKVEAVVWTVPILIIIFLAVLTWKTTHALEPSKPLAHDEKPITIEVVSMDWKWFFIYPEQGIATVNEIAFPANTPVYFKVTSNSVMNSFFIPRLGSQIYAMAGMQTRLHLIANEPGTYDGISASYSGPGFSGMKFKAIATPDRAAFDQWVAKAKQSPNTMSDMAAFEKLAAPSEYNQVEYFSNVKPDLFADVINKFMAHGKSMDMTQPEGEHSAHEGMEGMDMSHAESAH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	UBIQUINOL OXIDASE
Molecular weight formula_weight	22642.6 kDa
EC 编号 ec_number	1.10.3.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,H

MATDTLTHATAHAHEHGHHDAGGTKIFGFWIYLMSDCILFSILFATYAVLVNGTAGGPTGKDIFELPFVLVETFLLLFSSITYGMAAIAMYKNNKSQVISWLALTWLFGAGFIGMEIYEFHHLIVNGMGPDRSGFLSAFFALVGTHGLHVTSGLIWMAVLMVQIARRGLTSTNRTRIMCLSLFWHFLDVVWICVFTVVYLMGAM

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	UBIQUINOL OXIDASE
Molecular weight formula_weight	9294.4 kDa
EC 编号 ec_number	1.10.3.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,I

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	HEME O
Molecular weight formula_weight	838.9 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d1ffta_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.24 — Cytochrome c oxidase subunit I-like
Superfamily Superfamily superfamily	f.24.1 — Cytochrome c oxidase subunit I-like
Family Family family	f.24.1.1 — Cytochrome c oxidase subunit I-like

Domain ID domain_id	d1fftb1
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

Domain ID domain_id	d1fftb2
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.17 — Transmembrane helix hairpin
Superfamily Superfamily superfamily	f.17.2 — Cytochrome c oxidase subunit II-like, transmembrane region
Family Family family	f.17.2.1 — Cytochrome c oxidase subunit II-like, transmembrane region

Domain ID domain_id	d1fftc2
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.25 — Cytochrome c oxidase subunit III-like
Superfamily Superfamily superfamily	f.25.1 — Cytochrome c oxidase subunit III-like
Family Family family	f.25.1.1 — Cytochrome c oxidase subunit III-like

Domain ID domain_id	d1fftc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1fftf_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.24 — Cytochrome c oxidase subunit I-like
Superfamily Superfamily superfamily	f.24.1 — Cytochrome c oxidase subunit I-like
Family Family family	f.24.1.1 — Cytochrome c oxidase subunit I-like

Domain ID domain_id	d1fftg1
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

Domain ID domain_id	d1fftg2
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.17 — Transmembrane helix hairpin
Superfamily Superfamily superfamily	f.17.2 — Cytochrome c oxidase subunit II-like, transmembrane region
Family Family family	f.17.2.1 — Cytochrome c oxidase subunit II-like, transmembrane region

Domain ID domain_id	d1ffth2
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.25 — Cytochrome c oxidase subunit III-like
Superfamily Superfamily superfamily	f.25.1 — Cytochrome c oxidase subunit III-like
Family Family family	f.25.1.1 — Cytochrome c oxidase subunit III-like

Domain ID domain_id	d1ffth3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id	1fftA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	210 — Cytochrome C Oxidase; Chain A
Homologous superfamily homologous superfamily	10 — Cytochrome c oxidase-like, subunit I domain

Domain ID domain_id	1fftB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	1fftB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	1fftC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	80 — Cytochrome c oxidase, subunit III, four-helix bundle

Domain ID domain_id	1fftF00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	210 — Cytochrome C Oxidase; Chain A
Homologous superfamily homologous superfamily	10 — Cytochrome c oxidase-like, subunit I domain

Domain ID domain_id	1fftG01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	1fftG02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	1fftH00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	80 — Cytochrome c oxidase, subunit III, four-helix bundle

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Unit-cell length a length_a	92.100 Å
Unit-cell length b length_b	372.500 Å
Unit-cell length c length_c	232.700 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

The structure of ubiquinol oxidase from Escherichia coli

1. Protein Identity and Related Structures Protein Identity & Related Structures

UBIQUINOL OXIDASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

UBIQUINOL OXIDASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

UBIQUINOL OXIDASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1fft__assembly_1__model_1

1fft__assembly_1__model_1 | I(q)

1fft__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (10 domains)

CATH v4.4 (8 domains)

7. Citations (2)