SAXSdb — 5vjx

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

CLOCK-interacting pacemaker

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Circadian locomoter output cycles protein kaput × 4 （O08785） water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Circadian locomoter output cycles protein kaput × 4 （O08785） water × 6	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Circadian locomoter output cycles protein kaput × 4 （O08785） water × 6	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 6	Circadian locomoter output cycles protein kaput × 4 （O08785） water × 6	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 6	Circadian locomoter output cycles protein kaput × 4 （O08785） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CIPC_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–64； UniProt 352–414 Author chain D； PDBConstruct 2–64； UniProt 352–414 Author chain G； PDBConstruct 2–64； UniProt 352–414 Author chain J； PDBConstruct 2–64； UniProt 352–414 Author chain M； PDBConstruct 2–64； UniProt 352–414 Author chain R； PDBConstruct 2–64； UniProt 352–414 Author chain U； PDBConstruct 2–64； UniProt 352–414 Author chain X； PDBConstruct 2–64； UniProt 352–414 Author chain a； PDBConstruct 2–64； UniProt 352–414 Author chain d； PDBConstruct 2–64； UniProt 352–414

Circadian locomoter output cycles protein kaput

Mus musculus

UniProt O08785

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	CLOCK-interacting pacemaker × 2 （Q8R0W1） water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	CLOCK-interacting pacemaker × 2 （Q8R0W1） water × 6	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	CLOCK-interacting pacemaker × 2 （Q8R0W1） water × 6	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 6	CLOCK-interacting pacemaker × 2 （Q8R0W1） water × 6	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 6	CLOCK-interacting pacemaker × 2 （Q8R0W1） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CLOCK_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 6–51； UniProt 515–560 Author chain C； PDBConstruct 6–51； UniProt 515–560 Author chain E； PDBConstruct 6–51； UniProt 515–560 Author chain F； PDBConstruct 6–51； UniProt 515–560 Author chain H； PDBConstruct 6–51； UniProt 515–560 Author chain I； PDBConstruct 6–51； UniProt 515–560 Author chain K； PDBConstruct 6–51； UniProt 515–560 Author chain L； PDBConstruct 6–51； UniProt 515–560 Author chain N； PDBConstruct 6–51； UniProt 515–560 Author chain O； PDBConstruct 6–51； UniProt 515–560 Author chain S； PDBConstruct 6–51； UniProt 515–560 Author chain T； PDBConstruct 6–51； UniProt 515–560 Author chain V； PDBConstruct 6–51； UniProt 515–560 Author chain W； PDBConstruct 6–51； UniProt 515–560 Author chain Y； PDBConstruct 6–51； UniProt 515–560 Author chain Z； PDBConstruct 6–51； UniProt 515–560 Author chain b； PDBConstruct 6–51； UniProt 515–560 Author chain c； PDBConstruct 6–51； UniProt 515–560 Author chain e； PDBConstruct 6–51； UniProt 515–560 Author chain f； PDBConstruct 6–51； UniProt 515–560

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	5vjx
Deposition date deposition_date	2017-04-20
Structure title title	Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor
Keywords keywords	circadian rhythm, CLOCK protein, transcription activation, repressor, coiled coil, CIPC, circadian clock, TRANSFERASE; TRANSFERASE
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.

5vjx__assembly_1__model_1

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

Download this curve (.dat)

5vjx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5vjx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.93 Å
Rg (electron density)	22.59 Å
Total Rg	23.45 Å
Atom count	2205
Residues	256
Excluded volume	39301 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5vjx__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5vjx__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5vjx__assembly_3__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5vjx__assembly_4__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`5vjx__assembly_5__model_1`	hexameric （6）	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 (3)

Entity 1 Entity 1 polymer

Description description	CLOCK-interacting pacemaker
Molecular weight formula_weight	7205.1 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G,J,M,R,U,X,a,d
Atom count atom_count	12585

GNTLVVLHKSGLLEITLKTKELIRQNQATQAELDQLKEQTQMFIEATKSRAPQAWAKLQASLTS

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Circadian locomoter output cycles protein kaput
Molecular weight formula_weight	6196.4 kDa
EC 编号 ec_number	2.3.1.48
Source method src_method	man
Copy count entity_count	20

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C,E,F,H,I,K,L,N,O,S,T,V,W,Y,Z,b,c,e,f

GAMDPEFSAQLGAMQHLKDQLEQRTRMIEANIHRQQEELRKIQEQLQMVHG

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	338

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Unit-cell length a length_a	175.536 Å
Unit-cell length b length_b	116.836 Å
Unit-cell length c length_c	132.926 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	126.54 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	80

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

Resolution resolution	2.695 Å
Low-resolution limit resolution_low	47.307 Å
R factor r_factor	0.2208
R_work r_work	0.2179
R_free r_free	0.2749

Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor

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

CLOCK-interacting pacemaker

State in the Current Structure

Other States of the Same Protein in the Database

Circadian locomoter output cycles protein kaput

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

5vjx__assembly_1__model_1

5vjx__assembly_1__model_1 | I(q)

5vjx__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

7. Citations (1)

Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor

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

CLOCK-interacting pacemaker

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Circadian locomoter output cycles protein kaput

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

5vjx__assembly_1__model_1

5vjx__assembly_1__model_1 | I(q)

5vjx__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

7. Citations (1)