SAXSdb — 5mx7

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

Vitamin D3 receptor A

Danio rerio

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Nuclear receptor coactivator 1 × 2 （Q15788） 1a,20S-dihydroxyvitamin D3 × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VDRA_DANRE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A1； PDBConstruct 3–300； UniProt 156–453

Nuclear receptor coactivator 1

OrganismNot specified

UniProt Q15788

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Vitamin D3 receptor A × 2 （Q9PTN2） 1a,20S-dihydroxyvitamin D3 × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NCOA1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B1； PDBConstruct 1–15； UniProt 686–700

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	5mx7
Deposition date deposition_date	2017-01-21
Structure title title	1a,20S-dihydroxyvitamin D3 VDR complex
Keywords keywords	Vitamin D receptor, agonist, transcription; TRANSCRIPTION
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.

5mx7__assembly_1__model_1

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

Download this curve (.dat)

5mx7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5mx7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.61 Å
Rg (electron density)	27.13 Å
Total Rg	27.89 Å
Atom count	8174
Residues	496
Excluded volume	73004 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5mx7__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 (4)

Entity 1 Entity 1 polymer

Description description	Vitamin D3 receptor A
Molecular weight formula_weight	33916.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A1
Atom count atom_count	4145

HMLSDEQMQIINSLVEAHHKTYDDSYSDFVRFRPPVREGPVTRSASRAASLHSLSDASSDSFNHSPESVDTKLNFSNLLMMYQDSGSPDSSEEDQQSRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLEDMSWSCGGPDFKYCINDVTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMAICLLSPDRPGVQDHVRIEALQDRLCDVLQAYIRIQHPGGRLLYAKMIQKLADLRSLNEEHSKQYRSLSFQPEHSMQLTPLVLEVFGSEVS

Source Source

Source organism organism	Danio rerio
Common name common_name	Zebrafish
NCBI taxonomy ID ncbi_taxonomy_id	7955
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 polymer

Description description	Nuclear receptor coactivator 1
Molecular weight formula_weight	1776.1 kDa
EC 编号 ec_number	2.3.1.48
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B1

RHKILHRLLQEGSPS

Entity 3 Entity 3 non-polymer

Description description	1a,20S-dihydroxyvitamin D3
Molecular weight formula_weight	416.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	58

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Unit-cell length a length_a	65.936 Å
Unit-cell length b length_b	65.936 Å
Unit-cell length c length_c	262.970 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	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	1.980 Å
Low-resolution limit resolution_low	47.846 Å
R factor r_factor	0.2013
R_work r_work	0.2002
R_free r_free	0.2249

1a,20S-dihydroxyvitamin D3 VDR complex

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

Vitamin D3 receptor A

State in the Current Structure

Other States of the Same Protein in the Database

Nuclear receptor coactivator 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

5mx7__assembly_1__model_1

5mx7__assembly_1__model_1 | I(q)

5mx7__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

1a,20S-dihydroxyvitamin D3 VDR complex

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

Vitamin D3 receptor A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nuclear receptor coactivator 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

5mx7__assembly_1__model_1

5mx7__assembly_1__model_1 | I(q)

5mx7__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)