SAXSdb — 5cid

▼

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

Cytochrome c peroxidase, mitochondrial

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 iso-1 × 2 （P00044） HEME C × 4 2-methylaniline × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCPR_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–294； UniProt 68–361 Author chain C； PDBConstruct 1–294； UniProt 68–361

Cytochrome c iso-1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P00044

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 peroxidase, mitochondrial × 2 （P00431） HEME C × 4 2-methylaniline × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYC1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–108； UniProt 2–109 Author chain D； PDBConstruct 1–108； UniProt 2–109

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	5cid
Deposition date deposition_date	2015-07-12
Structure title title	Complex of yeast cytochrome c peroxidase (W191G) bound to o-toluidine with iso-1 cytochrome c
Keywords keywords	electron transfer, heme proteins, electron hopping, multi-step tunneling, photochemistry, ELECTRON TRANSPORT-OXIDOREDUCTASE complex; ELECTRON TRANSPORT/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.

5cid__assembly_1__model_1

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

Download this curve (.dat)

5cid__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5cid__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.73 Å
Rg (electron density)	29.79 Å
Total Rg	30.46 Å
Atom count	6604
Residues	804
Excluded volume	116930 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5cid__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	Cytochrome c peroxidase, mitochondrial
Molecular weight formula_weight	33396.1 kDa
EC 编号 ec_number	1.11.1.5
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	6613

TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKTHLKNSGYEGPGGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Cytochrome c iso-1
Molecular weight formula_weight	12073.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	2-methylaniline
Molecular weight formula_weight	107.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	9

▼

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5cida_
Class class	a — All alpha proteins
Fold Fold fold	a.93 — Heme-dependent peroxidases
Superfamily Superfamily superfamily	a.93.1 — Heme-dependent peroxidases
Family Family family	a.93.1.1 — CCP-like

Domain ID domain_id	d5cidb_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.1 — monodomain cytochrome c

Domain ID domain_id	d5cidc_
Class class	a — All alpha proteins
Fold Fold fold	a.93 — Heme-dependent peroxidases
Superfamily Superfamily superfamily	a.93.1 — Heme-dependent peroxidases
Family Family family	a.93.1.1 — CCP-like

Domain ID domain_id	d5cidd_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.1 — monodomain cytochrome c

CATH v4.4 (6 domains)

Domain ID domain_id	5cidA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	520 — Peroxidase; domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	5cidA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	420 — Peroxidase; domain 2
Homologous superfamily homologous superfamily	10 — Peroxidase, domain 2

Domain ID domain_id	5cidB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	5cidC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	520 — Peroxidase; domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	5cidC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	420 — Peroxidase; domain 2
Homologous superfamily homologous superfamily	10 — Peroxidase, domain 2

Domain ID domain_id	5cidD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

▶

Unit-cell length a length_a	45.380 Å
Unit-cell length b length_b	111.906 Å
Unit-cell length c length_c	87.894 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.33 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.763 Å
Low-resolution limit resolution_low	42.580 Å
R factor r_factor	0.2197
R_work r_work	0.2142
R_free r_free	0.2682

Complex of yeast cytochrome c peroxidase (W191G) bound to o-toluidine with iso-1 cytochrome c

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

Cytochrome c peroxidase, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

Cytochrome c iso-1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5cid__assembly_1__model_1

5cid__assembly_1__model_1 | I(q)

5cid__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Complex of yeast cytochrome c peroxidase (W191G) bound to o-toluidine with iso-1 cytochrome c

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

Cytochrome c peroxidase, mitochondrial

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 iso-1

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

5cid__assembly_1__model_1

5cid__assembly_1__model_1 | I(q)

5cid__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)