SAXSdb — 9rcg

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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 2	Nuclear receptor coactivator 2 × 1 （Q15596） 4-[4-[3-[5-[(3~{S})-4,4-dimethyl-3-oxidanyl-pentyl]-4-methyl-1,3-thiazol-2-yl]pentan-3-yl]phenoxy]-~{N}-oxidanyl-butanamide × 1 water × 2	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 A； PDBConstruct 5–302； UniProt 156–453

Nuclear receptor coactivator 2

OrganismNot specified

UniProt Q15596

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Vitamin D3 receptor A × 1 （Q9PTN2） 4-[4-[3-[5-[(3~{S})-4,4-dimethyl-3-oxidanyl-pentyl]-4-methyl-1,3-thiazol-2-yl]pentan-3-yl]phenoxy]-~{N}-oxidanyl-butanamide × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NCOA2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–13； UniProt 686–698

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	9rcg
Deposition date deposition_date	2025-05-28
Structure title title	Vitamin D receptor complex with a vitamin D receptor agonist/histone deacetylase inhibitor hybrid molecule
Keywords keywords	VDR complex, VDR ligand, superagonist, histone deacetylase inhibitor, 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.

9rcg__assembly_1__model_1

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

Download this curve (.dat)

9rcg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9rcg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.27 Å
Rg (electron density)	18.01 Å
Total Rg	19.10 Å
Atom count	2057
Residues	251
Excluded volume	36807 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9rcg__assembly_1__model_1`	dimeric （2）	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	34060.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2226

GSHMLSDEQMQIINSLVEAHHKTYDDSYSDFVRFRPPVREGPVTRSASRAASLHSLSDASSDSFNHSPESVDTKLNFSNLLMMYQDSGSPDSSEEDQQSRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLEDMSWSCGGPDFKYCINDVTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMAICLLSPDRPGVQDHVRIEALQDRLCDVLQAYIRIQHPGGRLLYAKMIQKLADLRSLNEEHSKQYRSLSFQPEHSMQLTPLVLEVFGSEVS

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

Entity 2 Entity 2 polymer

Description description	Nuclear receptor coactivator 2
Molecular weight formula_weight	1579.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

KHKILHRLLQDSS

Entity 3 Entity 3 non-polymer

Description description	4-[4-[3-[5-[(3~{S})-4,4-dimethyl-3-oxidanyl-pentyl]-4-methyl-1,3-thiazol-2-yl]pentan-3-yl]phenoxy]-~{N}-oxidanyl-butanamide
Molecular weight formula_weight	476.7 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	169

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Unit-cell length a length_a	66.020 Å
Unit-cell length b length_b	66.020 Å
Unit-cell length c length_c	262.510 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	hexagonal

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	22.020 Å
R factor r_factor	0.1764
R_work r_work	0.1764
R_free r_free	0.2060

Vitamin D receptor complex with a vitamin D receptor agonist/histone deacetylase inhibitor hybrid molecule

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 2

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

9rcg__assembly_1__model_1

9rcg__assembly_1__model_1 | I(q)

9rcg__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)

Vitamin D receptor complex with a vitamin D receptor agonist/histone deacetylase inhibitor hybrid molecule

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 2

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

9rcg__assembly_1__model_1

9rcg__assembly_1__model_1 | I(q)

9rcg__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)