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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 352–414 Chain a； UniProt 352–414	Fragment：UNP Residues 352-414 Non-standard monomer：Yes (specific site not provided by mmCIF)	Circadian locomoter output cycles protein kaput × 4 （O08785）	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 8；291 K；100mM Hepes pH 8.0, 200mM Proline, 15% PEG3350, 3% myo-Inositiol (w/v)	Resolution 2.69 Å R-free 0.275
2	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain D； UniProt 352–414 Chain J； UniProt 352–414	Fragment：UNP Residues 352-414 Non-standard monomer：Yes (specific site not provided by mmCIF)	Circadian locomoter output cycles protein kaput × 4 （O08785）	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 8；291 K；100mM Hepes pH 8.0, 200mM Proline, 15% PEG3350, 3% myo-Inositiol (w/v)	Resolution 2.69 Å R-free 0.275
3	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain G； UniProt 352–414 Chain U； UniProt 352–414	Fragment：UNP Residues 352-414 Non-standard monomer：Yes (specific site not provided by mmCIF)	Circadian locomoter output cycles protein kaput × 4 （O08785）	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 8；291 K；100mM Hepes pH 8.0, 200mM Proline, 15% PEG3350, 3% myo-Inositiol (w/v)	Resolution 2.69 Å R-free 0.275
4	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain M； UniProt 352–414 Chain R； UniProt 352–414	Fragment：UNP Residues 352-414 Non-standard monomer：Yes (specific site not provided by mmCIF)	Circadian locomoter output cycles protein kaput × 4 （O08785）	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 8；291 K；100mM Hepes pH 8.0, 200mM Proline, 15% PEG3350, 3% myo-Inositiol (w/v)	Resolution 2.69 Å R-free 0.275
5	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain X； UniProt 352–414 Chain d； UniProt 352–414	Fragment：UNP Residues 352-414 Non-standard monomer：Yes (specific site not provided by mmCIF)	Circadian locomoter output cycles protein kaput × 4 （O08785）	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 8；291 K；100mM Hepes pH 8.0, 200mM Proline, 15% PEG3350, 3% myo-Inositiol (w/v)	Resolution 2.69 Å R-free 0.275

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5VJX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5VJI Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor Deposited 2017-04-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 352–414（63 aa） Fragment：UNP residues 352-414	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.3；291 K；100mM Bis-tris pH7.3 27% PEG2000MME 1% beat-DDM	Resolution 1.86 Å R-free 0.280
5VJI Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor Deposited 2017-04-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 352–414（63 aa） Fragment：UNP residues 352-414	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.3；291 K；100mM Bis-tris pH7.3 27% PEG2000MME 1% beat-DDM	Resolution 1.86 Å R-free 0.280

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain B； UniProt 515–560 Chain C； UniProt 515–560 Chain b； UniProt 515–560 Chain c； UniProt 515–560	Fragment：UNP Residues 516-560 Non-standard monomer：Yes (specific site not provided by mmCIF)	CLOCK-interacting pacemaker × 2 （Q8R0W1）	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 8；291 K；100mM Hepes pH 8.0, 200mM Proline, 15% PEG3350, 3% myo-Inositiol (w/v)	Resolution 2.69 Å R-free 0.275
2	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain E； UniProt 515–560 Chain F； UniProt 515–560 Chain K； UniProt 515–560 Chain L； UniProt 515–560	Fragment：UNP Residues 516-560 Non-standard monomer：Yes (specific site not provided by mmCIF)	CLOCK-interacting pacemaker × 2 （Q8R0W1）	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 8；291 K；100mM Hepes pH 8.0, 200mM Proline, 15% PEG3350, 3% myo-Inositiol (w/v)	Resolution 2.69 Å R-free 0.275
3	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain H； UniProt 515–560 Chain I； UniProt 515–560 Chain V； UniProt 515–560 Chain W； UniProt 515–560	Fragment：UNP Residues 516-560 Non-standard monomer：Yes (specific site not provided by mmCIF)	CLOCK-interacting pacemaker × 2 （Q8R0W1）	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 8；291 K；100mM Hepes pH 8.0, 200mM Proline, 15% PEG3350, 3% myo-Inositiol (w/v)	Resolution 2.69 Å R-free 0.275
4	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain N； UniProt 515–560 Chain O； UniProt 515–560 Chain S； UniProt 515–560 Chain T； UniProt 515–560	Fragment：UNP Residues 516-560 Non-standard monomer：Yes (specific site not provided by mmCIF)	CLOCK-interacting pacemaker × 2 （Q8R0W1）	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 8；291 K；100mM Hepes pH 8.0, 200mM Proline, 15% PEG3350, 3% myo-Inositiol (w/v)	Resolution 2.69 Å R-free 0.275
5	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain Y； UniProt 515–560 Chain Z； UniProt 515–560 Chain e； UniProt 515–560 Chain f； UniProt 515–560	Fragment：UNP Residues 516-560 Non-standard monomer：Yes (specific site not provided by mmCIF)	CLOCK-interacting pacemaker × 2 （Q8R0W1）	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 8；291 K；100mM Hepes pH 8.0, 200mM Proline, 15% PEG3350, 3% myo-Inositiol (w/v)	Resolution 2.69 Å R-free 0.275

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5VJX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4F3L Crystal Structure of the Heterodimeric CLOCK:BMAL1 Transcriptional Activator Complex Deposited 2012-05-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–384（359 aa） Fragment：UNP residues 26-384	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；100 mM Hepes pH 8.0, 6% PEG 3350 and 75 mM NaF., VAPOR DIFFUSION, temperature 293K	Resolution 2.27 Å R-free 0.217
5VJI Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor Deposited 2017-04-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 516–560（45 aa） Fragment：UNP Residues 516-560 Chain B 516–560（45 aa） Fragment：UNP Residues 516-560	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.3；291 K；100mM Bis-tris pH7.3 27% PEG2000MME 1% beat-DDM	Resolution 1.86 Å R-free 0.280
5VJI Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor Deposited 2017-04-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 516–560（45 aa） Fragment：UNP Residues 516-560 Chain E 516–560（45 aa） Fragment：UNP Residues 516-560	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.3；291 K；100mM Bis-tris pH7.3 27% PEG2000MME 1% beat-DDM	Resolution 1.86 Å R-free 0.280
8OSJ Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL-6.2 (DNA conformation 1) Deposited 2023-04-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain M 26–395（370 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.20 Å
8OSK Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL+5.8 (composite map) Deposited 2023-04-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain M 26–395（370 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8OSL Cryo-EM structure of CLOCK-BMAL1 bound to the native Por enhancer nucleosome (map 2, additional 3D classification and flexible refinement) Deposited 2023-04-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric	Chain M 26–395（370 aa） Chain O 26–395（370 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.90 Å

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	45.72 Å
Radius of gyration Rg (electron density) rg_electron	45.45 Å
Forward intensity I(0) i0	533680000.00
Molecular weight molecular_weight	178060.0 kDa
Excluded volume excluded_volume	217390 Å³
Envelope volume envelope_volume	336020 Å³
Hydration-shell volume shell_volume	61054 Å³
Envelope diameter envelope_diameter	150.4 Å
Shell Rg shell_rg	50.54 Å
Envelope Rg envelope_rg	44.71 Å
Shape Rg shape_rg	45.43 Å
Total Rg total_rg	45.73 Å
Total atoms total_atoms	12210
Residues n_residues	1421
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	148.6 Å
Rg (real space) rg_real	45.58 Å
Rg uncertainty (real space) rg_real_error	1.17 Å
I(0) (real space) i0_real	5.3370e+08
I(0) uncertainty (real space) i0_real_error	9.8920e+06
Rg (reciprocal space) rg_reciprocal	45.72 Å
I(0) (reciprocal space) i0_reciprocal	533800000.0000
Solution quality estimate total_estimate	0.9015
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	61.2 Å
Skewness Skewness skewness	0.128
Kurtosis Kurtosis kurtosis	-0.660
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	46060000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.917

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 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

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 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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8. Citations (1)

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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

fit	/app/data/saxs_computation/vj/5vjx/5vjx.fit
pddf	/app/data/pr_computation/vj/5vjx/5vjx.pr.out
profile	/app/data/saxs_computation/vj/5vjx/5vjx.dat

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)