1m56

Structure of cytochrome c oxidase from Rhodobactor sphaeroides (Wild Type)

Method: X-RAY DIFFRACTION

▼

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

CYTOCHROME C OXIDASE

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	CYTOCHROME C OXIDASE × 1 （Q03736） CYTOCHROME C OXIDASE × 1 （P84153） CYTOCHROME C OXIDASE × 1 （Q8KRK5） COPPER (II) ION × 3 MAGNESIUM ION × 1 CALCIUM ION × 1 HEME-A × 2 1,2-Distearoyl-sn-glycerophosphoethanolamine × 6 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	CYTOCHROME C OXIDASE × 1 （Q03736） CYTOCHROME C OXIDASE × 1 （P84153） CYTOCHROME C OXIDASE × 1 （Q8KRK5） COPPER (II) ION × 3 MAGNESIUM ION × 1 CALCIUM ION × 1 HEME-A × 2 1,2-Distearoyl-sn-glycerophosphoethanolamine × 6 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COX1_RHOSH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–566； UniProt 1–566 Author chain G； PDBConstruct 1–566； UniProt 1–566

CYTOCHROME C OXIDASE

OrganismNot specified

UniProt Q03736

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	CYTOCHROME C OXIDASE × 1 （P33517） CYTOCHROME C OXIDASE × 1 （P84153） CYTOCHROME C OXIDASE × 1 （Q8KRK5） COPPER (II) ION × 3 MAGNESIUM ION × 1 CALCIUM ION × 1 HEME-A × 2 1,2-Distearoyl-sn-glycerophosphoethanolamine × 6 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	CYTOCHROME C OXIDASE × 1 （P33517） CYTOCHROME C OXIDASE × 1 （P84153） CYTOCHROME C OXIDASE × 1 （Q8KRK5） COPPER (II) ION × 3 MAGNESIUM ION × 1 CALCIUM ION × 1 HEME-A × 2 1,2-Distearoyl-sn-glycerophosphoethanolamine × 6 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COX2_RHOSH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–264； UniProt 26–289 Author chain H； PDBConstruct 1–264； UniProt 26–289

CYTOCHROME C OXIDASE

OrganismNot specified

UniProt P84153

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	CYTOCHROME C OXIDASE × 1 （P33517） CYTOCHROME C OXIDASE × 1 （Q03736） CYTOCHROME C OXIDASE × 1 （Q8KRK5） COPPER (II) ION × 3 MAGNESIUM ION × 1 CALCIUM ION × 1 HEME-A × 2 1,2-Distearoyl-sn-glycerophosphoethanolamine × 6 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	CYTOCHROME C OXIDASE × 1 （P33517） CYTOCHROME C OXIDASE × 1 （Q03736） CYTOCHROME C OXIDASE × 1 （Q8KRK5） COPPER (II) ION × 3 MAGNESIUM ION × 1 CALCIUM ION × 1 HEME-A × 2 1,2-Distearoyl-sn-glycerophosphoethanolamine × 6 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P84153_RHOSH
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–266； UniProt 1–266 Author chain I； PDBConstruct 1–266； UniProt 1–266

CYTOCHROME C OXIDASE

OrganismNot specified

UniProt Q8KRK5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	CYTOCHROME C OXIDASE × 1 （P33517） CYTOCHROME C OXIDASE × 1 （Q03736） CYTOCHROME C OXIDASE × 1 （P84153） COPPER (II) ION × 3 MAGNESIUM ION × 1 CALCIUM ION × 1 HEME-A × 2 1,2-Distearoyl-sn-glycerophosphoethanolamine × 6 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	CYTOCHROME C OXIDASE × 1 （P33517） CYTOCHROME C OXIDASE × 1 （Q03736） CYTOCHROME C OXIDASE × 1 （P84153） COPPER (II) ION × 3 MAGNESIUM ION × 1 CALCIUM ION × 1 HEME-A × 2 1,2-Distearoyl-sn-glycerophosphoethanolamine × 6 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8KRK5_RHOSH
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–51； UniProt 11–61 Author chain J； PDBConstruct 1–51； UniProt 11–61

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1m56
Deposition date deposition_date	2002-07-08
Structure title title	Structure of cytochrome c oxidase from Rhodobactor sphaeroides (Wild Type)
Keywords keywords	Membrane Protein, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1m56__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1m56__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1m56__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	31.93 Å
Rg (electron density)	30.46 Å
Total Rg	31.15 Å
Atom count	9249
Residues	1114
Excluded volume	168950 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1m56__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1m56__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	CYTOCHROME C OXIDASE
Molecular weight formula_weight	63195.4 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,G
Atom count atom_count	18934

MADAAIHGHEHDRRGFFTRWFMSTNHKDIGVLYLFTGGLVGLISVAFTVYMRMELMAPGVQFMCAEHLESGLVKGFFQSLWPSAVENCTPNGHLWNVMITGHGILMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRMNNLSYWLYVAGTSLAVASLFAPGGNGQLGSGIGWVLYPPLSTSESGYSTDLAIFAVHLSGASSILGAINMITTFLNMRAPGMTMHKVPLFAWSIFVTAWLILLALPVLAGAITMLLTDRNFGTTFFQPSGGGDPVLYQHILWFFGHPEVYIIVLPAFGIVSHVIATFAKKPIFGYLPMVYAMVAIGVLGFVVWAHHMYTAGLSLTQQSYFMMATMVIAVPTGIKIFSWIATMWGGSIELKTPMLWALGFLFLFTVGGVTGIVLSQASVDRYYHDTYYVVAHFHYVMSLGAVFGIFAGIYFWIGKMSGRQYPEWAGKLHFWMMFVGANLTFFPQHFLGRQGMPRRYIDYPEAFATWNFVSSLGAFLSFASFLFFLGVIFYTLTRGARVTANNYWNEHADTLEWTLTSPPPEHTFEQLPKREDWERAPAH

Entity 2 Entity 2 polymer

Description description	CYTOCHROME C OXIDASE
Molecular weight formula_weight	29385.4 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,H

QQQSLEIIGRPQPGGTGFQPSASPVATQIHWLDGFILVIIAAITIFVTLLILYAVWRFHEKRNKVPARFTHNSPLEIAWTIVPIVILVAIGAFSLPVLFNQQEIPEADVTVKVTGYQWYWGYEYPDEEISFESYMIGSPATGGDNRMSPEVEQQLIEAGYSRDEFLLATDTAMVVPVNKTVVVQVTGADVIHSWTVPAFGVKQDAVPGRLAQLWFRAEREGIFFGQCSELCGISHAYMPITVKVVSEEAYAAWLEQARGGTYEL

Entity 3 Entity 3 polymer

Description description	CYTOCHROME C OXIDASE
Molecular weight formula_weight	30197.2 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,I

MAHAKNHDYHILPPSIWPFMASVGAFVMLFGAVLWMHGSGPWMGLIGLVVVLYTMFGWWSDVVTESLEGDHTPVVRLGLRWGFILFIMSEVMFFSAWFWSFFKHALYPMGPESPIIDGIFPPEGIITFDPWHLPLINTLILLCSGCAATWAHHALVHENNRRDVAWGLALAIALGALFTVFQAYEYSHAAFGFAGNIYGANFFMATGFHGFHVIVGTIFLLVCLIRVQRGHFTPEKHVGFEAAIWYWHFVDVVWLFLFASIYIWGQ

Entity 4 Entity 4 polymer

Description description	CYTOCHROME C OXIDASE
Molecular weight formula_weight	5409.3 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	D,J

MADHSHPAHGHVAGSMDITQQEKTFAGFVRMVTWAAVVIVAALIFLALANA

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	6

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	HEME-A
Molecular weight formula_weight	852.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 9 Entity 9 non-polymer

Description description	1,2-Distearoyl-sn-glycerophosphoethanolamine
Molecular weight formula_weight	748.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	436

▼

6. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d1m56a_
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	d1m56b1
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	d1m56b2
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	d1m56c_
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	d1m56d_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.8 — Bacterial aa3 type cytochrome c oxidase subunit IV
Family Family family	f.23.8.1 — Bacterial aa3 type cytochrome c oxidase subunit IV

Domain ID domain_id	d1m56g_
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	d1m56h1
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	d1m56h2
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	d1m56i_
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	d1m56j_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.8 — Bacterial aa3 type cytochrome c oxidase subunit IV
Family Family family	f.23.8.1 — Bacterial aa3 type cytochrome c oxidase subunit IV

CATH v4.4 (12 domains)

Domain ID domain_id	1m56A00
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	1m56B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	1m56B02
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	1m56C01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	1m56C02
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	1m56D00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	160 — Bacterial aa3 type cytochrome c oxidase subunit IV

Domain ID domain_id	1m56G00
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	1m56H01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	1m56H02
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	1m56I01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	1m56I02
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	1m56J00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	160 — Bacterial aa3 type cytochrome c oxidase subunit IV

▶

Unit-cell length a length_a	340.360 Å
Unit-cell length b length_b	340.360 Å
Unit-cell length c length_c	89.668 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2360
R_work r_work	0.2360
R_free r_free	0.2750

Structure of cytochrome c oxidase from Rhodobactor sphaeroides (Wild Type)

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

CYTOCHROME C 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

CYTOCHROME C 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

CYTOCHROME C 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

CYTOCHROME C 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

1m56__assembly_2__model_1

1m56__assembly_2__model_1 | I(q)

1m56__assembly_2__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 (10)

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 polymer

Polymer 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 water

6. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (10 domains)

CATH v4.4 (12 domains)

7. Citations (1)