2yev

Structure of caa3-type cytochrome oxidase

Method: X-RAY DIFFRACTION

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

CYTOCHROME C OXIDASE POLYPEPTIDE I+III

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	CYTOCHROME C OXIDASE SUBUNIT 2 × 1 （Q5SLI2） CAA3-TYPE CYTOCHROME OXIDASE SUBUNIT IV × 1 （Q5SH67） ;(1R,4S,6R)-6-({[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OXY}METHYL)-4-HYDROXY-1-{[(15-METHYLHEXADECANOYL)OXY]METHYL}-4-OXIDO-7-OXO-3,5-DIOXA-8-AZA-4-PHOSPHAHEPTACOS-1-YL 15-METHYLHEXADECANOATE ; × 1 HEME-AS × 2 COPPER (II) ION × 1 MAGNESIUM ION × 1 DINUCLEAR COPPER ION × 1 HEME C × 1 CHLORIDE ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	CYTOCHROME C OXIDASE SUBUNIT 2 × 1 （Q5SLI2） CAA3-TYPE CYTOCHROME OXIDASE SUBUNIT IV × 1 （Q5SH67） ;(1R,4S,6R)-6-({[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OXY}METHYL)-4-HYDROXY-1-{[(15-METHYLHEXADECANOYL)OXY]METHYL}-4-OXIDO-7-OXO-3,5-DIOXA-8-AZA-4-PHOSPHAHEPTACOS-1-YL 15-METHYLHEXADECANOATE ; × 1 HEME-AS × 2 COPPER (II) ION × 1 (2R)-3-HYDROXYPROPANE-1,2-DIYL DIHEXADECANOATE × 1 (2R)-2,3-DIHYDROXYPROPYL (7Z)-TETRADEC-7-ENOATE × 2 MAGNESIUM ION × 1 DINUCLEAR COPPER ION × 1 HEME C × 1 1,3-DIHYDROXYPROPAN-2-YL (Z)-TETRADEC-7-ENOATE × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COX13_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–791； UniProt 1–791 Author chain D； PDBConstruct 1–791； UniProt 1–791

CYTOCHROME C OXIDASE SUBUNIT 2

OrganismNot specified

UniProt Q5SLI2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	CYTOCHROME C OXIDASE POLYPEPTIDE I+III × 1 （P98005） CAA3-TYPE CYTOCHROME OXIDASE SUBUNIT IV × 1 （Q5SH67） ;(1R,4S,6R)-6-({[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OXY}METHYL)-4-HYDROXY-1-{[(15-METHYLHEXADECANOYL)OXY]METHYL}-4-OXIDO-7-OXO-3,5-DIOXA-8-AZA-4-PHOSPHAHEPTACOS-1-YL 15-METHYLHEXADECANOATE ; × 1 HEME-AS × 2 COPPER (II) ION × 1 MAGNESIUM ION × 1 DINUCLEAR COPPER ION × 1 HEME C × 1 CHLORIDE ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	CYTOCHROME C OXIDASE POLYPEPTIDE I+III × 1 （P98005） CAA3-TYPE CYTOCHROME OXIDASE SUBUNIT IV × 1 （Q5SH67） ;(1R,4S,6R)-6-({[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OXY}METHYL)-4-HYDROXY-1-{[(15-METHYLHEXADECANOYL)OXY]METHYL}-4-OXIDO-7-OXO-3,5-DIOXA-8-AZA-4-PHOSPHAHEPTACOS-1-YL 15-METHYLHEXADECANOATE ; × 1 HEME-AS × 2 COPPER (II) ION × 1 (2R)-3-HYDROXYPROPANE-1,2-DIYL DIHEXADECANOATE × 1 (2R)-2,3-DIHYDROXYPROPYL (7Z)-TETRADEC-7-ENOATE × 2 MAGNESIUM ION × 1 DINUCLEAR COPPER ION × 1 HEME C × 1 1,3-DIHYDROXYPROPAN-2-YL (Z)-TETRADEC-7-ENOATE × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5SLI2_THET8
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–337； UniProt 1–337 Author chain E； PDBConstruct 1–337； UniProt 1–337

CAA3-TYPE CYTOCHROME OXIDASE SUBUNIT IV

OrganismNot specified

UniProt Q5SH67

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	CYTOCHROME C OXIDASE POLYPEPTIDE I+III × 1 （P98005） CYTOCHROME C OXIDASE SUBUNIT 2 × 1 （Q5SLI2） ;(1R,4S,6R)-6-({[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OXY}METHYL)-4-HYDROXY-1-{[(15-METHYLHEXADECANOYL)OXY]METHYL}-4-OXIDO-7-OXO-3,5-DIOXA-8-AZA-4-PHOSPHAHEPTACOS-1-YL 15-METHYLHEXADECANOATE ; × 1 HEME-AS × 2 COPPER (II) ION × 1 MAGNESIUM ION × 1 DINUCLEAR COPPER ION × 1 HEME C × 1 CHLORIDE ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	CYTOCHROME C OXIDASE POLYPEPTIDE I+III × 1 （P98005） CYTOCHROME C OXIDASE SUBUNIT 2 × 1 （Q5SLI2） ;(1R,4S,6R)-6-({[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OXY}METHYL)-4-HYDROXY-1-{[(15-METHYLHEXADECANOYL)OXY]METHYL}-4-OXIDO-7-OXO-3,5-DIOXA-8-AZA-4-PHOSPHAHEPTACOS-1-YL 15-METHYLHEXADECANOATE ; × 1 HEME-AS × 2 COPPER (II) ION × 1 (2R)-3-HYDROXYPROPANE-1,2-DIYL DIHEXADECANOATE × 1 (2R)-2,3-DIHYDROXYPROPYL (7Z)-TETRADEC-7-ENOATE × 2 MAGNESIUM ION × 1 DINUCLEAR COPPER ION × 1 HEME C × 1 1,3-DIHYDROXYPROPAN-2-YL (Z)-TETRADEC-7-ENOATE × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5SH67_THET8
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–66； UniProt 1–66 Author chain F； PDBConstruct 1–66； UniProt 1–66

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	2yev
Deposition date deposition_date	2011-03-31
Structure title title	Structure of caa3-type cytochrome oxidase
Keywords keywords	ELECTRON TRANSPORT; ELECTRON TRANSPORT
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.

2yev__assembly_1__model_1

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

Download this curve (.dat)

2yev__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2yev__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.72 Å
Rg (electron density)	31.49 Å
Total Rg	32.18 Å
Atom count	9539
Residues	1161
Excluded volume	173890 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2yev__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2yev__assembly_2__model_1`	trimeric （3）	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 (14)

Entity 1 Entity 1 polymer

Description description	CYTOCHROME C OXIDASE POLYPEPTIDE I+III
Molecular weight formula_weight	89281.1 kDa
EC 编号 ec_number	1.9.3.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	19587

MAITAKPKAGVWAVLWDLLTTVDHKKIGLMYTATAFFAFALAGVFSLLIRTQLAVPNNQFLTGEQYNQILTLHGATMLFFFIIQAGLTGFGNFVVPLMLGARDVALPRVNAFSYWAFLGAIVLALMSYFFPGGAPSVGWTFYYPFSAQSESGVDFYLAAILLLGFSSLLGNANFVATIYNLRAQGMSLWKMPIYVWSVFAASVLNLFSLAGLTAATLLVLLERKIGLSWFNPAVGGDPVLFQQFFWFYSHPTVYVMLLPYLGILAEVASTFARKPLFGYRQMVWAQMGIVVLGTMVWAHHMFTVGESTLFQIAFAFFTALIAVPTGVKLFNIIGTLWGGKLQMKTPLYWVLGFIFNFLLGGITGVMLSMTPLDYQFHDSYFVVAHFHNVLMAGSGFGAFAGLYYWWPKMTGRMYDERLGRLHFWLFLVGYLLTFLPQYALGYLGMPRRYYTYNADIAGWPELNLLSTIGAYILGLGGLVWIYTMWKSLRSGPKAPDNPWGGYTLEWLTASPPKAHNFDVKLPTEFPSERPLYDWKKKGVELKPEDPAHIHLPNSSFWPFYSAATLFAFFVAVAALPVPNVWMWVFLALFAYGLVRWALEDEYSHPVEHHTVTGKSNAWMGMAWFIVSEVGLFAILIAGYLYLRLSGAATPPEERPALWLALLNTFLLVSSSFTVHFAHHDLRRGRFNPFRFGLLVTIILGVLFFLVQSWEFYQFYHHSSWQENLWTAAFFTIVGLHGLHVVIGGFGLILAYLQALRGKITLHNHGTLEAASMYWHLVDAVWLVIVTIFYVW

Entity 2 Entity 2 polymer

Description description	CYTOCHROME C OXIDASE SUBUNIT 2
Molecular weight formula_weight	37388.0 kDa
EC 编号 ec_number	1.9.3.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

MQRSFAALGLWGLSLAQEAHRVAITHPGGSFNQEVAFLFPWVYFFSFLIFLVVAGSLAYVTWKFRARPEDQEEPPQIHGNDRLEVVWTLIPLAIVFVLFGLTAKALIQVNRPIPGAMKVEVTGYQFWWDFHYPELGLRNSNELVLPAGVPVELEITSKDVIHSFWVPGLAGKRDAIPGQTTRISFEPKEPGLYYGFCAELCGASHARMLFRVVVLPKEEFDRFVEAAKASPAPVADERGQQVFQQNCAACHGVARSMPPAVIGPELGLWGNRTSLGAGIVENTPENLKAWIRDPAGMKPGVKMPGFPQLSEEDLDALVRYLEGLKVEGFDFGALPKF

Entity 3 Entity 3 polymer

Description description	CAA3-TYPE CYTOCHROME OXIDASE SUBUNIT IV
Molecular weight formula_weight	7354.0 kDa
EC 编号 ec_number	1.9.3.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

MVYIALFALGAALVTLFFYLILNPRVLTTEGETFDLRFVLFMLLLILLAAGTVALMLLIGKAHHLL

Entity 4 Entity 4 non-polymer

Description description	;(1R,4S,6R)-6-({[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OXY}METHYL)-4-HYDROXY-1-{[(15-METHYLHEXADECANOYL)OXY]METHYL}-4-OXIDO-7-OXO-3,5-DIOXA-8-AZA-4-PHOSPHAHEPTACOS-1-YL 15-METHYLHEXADECANOATE ;
Molecular weight formula_weight	1233.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	HEME-AS
Molecular weight formula_weight	921.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 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 7 Entity 7 non-polymer

Description description	(2R)-3-HYDROXYPROPANE-1,2-DIYL DIHEXADECANOATE
Molecular weight formula_weight	568.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	(2R)-2,3-DIHYDROXYPROPYL (7Z)-TETRADEC-7-ENOATE
Molecular weight formula_weight	300.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	DINUCLEAR COPPER ION
Molecular weight formula_weight	127.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 12 Entity 12 non-polymer

Description description	1,3-DIHYDROXYPROPAN-2-YL (Z)-TETRADEC-7-ENOATE
Molecular weight formula_weight	300.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 13 Entity 13 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 14 Entity 14 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	392

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	2yevA01
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	2yevA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	2yevA03
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	2yevB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	2yevB02
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	2yevC00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2yevD01
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	2yevD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	2yevD03
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	2yevE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	2yevE02
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	2yevF00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	110 —

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Unit-cell length a length_a	127.250 Å
Unit-cell length b length_b	76.030 Å
Unit-cell length c length_c	300.267 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.21 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.360 Å
Low-resolution limit resolution_low	77.179 Å
R factor r_factor	0.1736
R_work r_work	0.1712
R_free r_free	0.2183

Structure of caa3-type cytochrome oxidase

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

CYTOCHROME C OXIDASE POLYPEPTIDE I+III

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CYTOCHROME C OXIDASE SUBUNIT 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CAA3-TYPE CYTOCHROME OXIDASE SUBUNIT IV

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

2yev__assembly_1__model_1

2yev__assembly_1__model_1 | I(q)

2yev__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (14)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 non-polymer

Entity 14 Entity 14 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)