SAXSdb — 7bbt

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

Cytochrome c iso-1

Saccharomyces cerevisiae S288C

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	HEME C × 4 ;4-[[49,50,51,52,53,54,55,56-octahydroxy-11,17,23,29,35,41,47-heptakis[(4-sulfonatophenyl)methyl]-5-nonacyclo[43.3.1.13,7.19,13.115,19.121,25.127,31.133,37.139,43]hexapentaconta-1(49),3,5,7(56),9,11,13(55),15,17,19(54),21,23,25(53),27,29,31(52),33,35,37(51),39,41,43(50),45,47-tetracosaenyl]methyl]benzenesulfonate ; × 3 POLYETHYLENE GLYCOL (N=34) × 1 water × 4	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	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–108； UniProt 3–109 Author chain B； PDBConstruct 2–108； UniProt 3–109 Author chain C； PDBConstruct 2–108； UniProt 3–109 Author chain D； PDBConstruct 2–108； UniProt 3–109

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7bbt
Deposition date deposition_date	2020-12-18
Structure title title	Structure of cytochrome c in complex with a p-benzyl-sulfonato-calix[8]arene-PEG pseudorotaxane
Keywords keywords	extended-arm, molecular recognition, biohybrid, alpha-helix, 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.

7bbt__assembly_1__model_1

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

Download this curve (.dat)

7bbt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7bbt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.58 Å
Rg (electron density)	25.67 Å
Total Rg	26.64 Å
Atom count	4079
Residues	428
Excluded volume	73195 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7bbt__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	Cytochrome c iso-1
Molecular weight formula_weight	12041.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4134

AEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKATE

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	;4-[[49,50,51,52,53,54,55,56-octahydroxy-11,17,23,29,35,41,47-heptakis[(4-sulfonatophenyl)methyl]-5-nonacyclo[43.3.1.13,7.19,13.115,19.121,25.127,31.133,37.139,43]hexapentaconta-1(49),3,5,7(56),9,11,13(55),15,17,19(54),21,23,25(53),27,29,31(52),33,35,37(51),39,41,43(50),45,47-tetracosaenyl]methyl]benzenesulfonate ;
Molecular weight formula_weight	2202.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	POLYETHYLENE GLYCOL (N=34)
Molecular weight formula_weight	1529.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	40

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7bbtA01
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	7bbtB01
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	7bbtC01
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	7bbtD01
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

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Unit-cell length a length_a	120.851 Å
Unit-cell length b length_b	70.215 Å
Unit-cell length c length_c	70.175 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.93 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	3.023 Å
Low-resolution limit resolution_low	50.570 Å
R factor r_factor	0.2346
R_work r_work	0.2334
R_free r_free	0.2606

Structure of cytochrome c in complex with a p-benzyl-sulfonato-calix[8]arene-PEG pseudorotaxane

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

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

7bbt__assembly_1__model_1

7bbt__assembly_1__model_1 | I(q)

7bbt__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Structure of cytochrome c in complex with a p-benzyl-sulfonato-calix[8]arene-PEG pseudorotaxane

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

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

7bbt__assembly_1__model_1

7bbt__assembly_1__model_1 | I(q)

7bbt__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)