← Back to search

9rcg

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

Method: X-RAY DIFFRACTION D_max: 62.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9rcg
deposition_date	2025-05-28
title	Vitamin D receptor complex with a vitamin D receptor agonist/histone deacetylase inhibitor hybrid molecule
keywords	VDR complex, VDR ligand, superagonist, histone deacetylase inhibitor, TRANSCRIPTION; TRANSCRIPTION
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	19.02 Å
rg_electron	18.01 Å
i0	28062000.00
molecular_weight	27181.0 kDa
excluded_volume	26312 Å³
envelope_volume	41949 Å³
shell_volume	19242 Å³
envelope_diameter	64.0 Å
shell_rg	24.51 Å
envelope_rg	18.36 Å
shape_rg	17.97 Å
total_rg	18.79 Å
total_atoms	2057
n_residues	251
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

▼

3. P(r) Analysis (GNOM)

dmax	62.3 Å
rg_real	18.92 Å
rg_real_error	0.38 Å
i0_real	2.8060e+07
i0_real_error	3.3610e+05
rg_reciprocal	18.94 Å
i0_reciprocal	28060000.0000
total_estimate	0.8042
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	24.2 Å
skewness	0.233
kurtosis	-0.296
angular_range	— – 0.4200 Å⁻¹
current_alpha	0.0000
highest_alpha	6098000.0000
n_real_points	73
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.817; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	Vitamin D3 receptor A
formula_weight	34060.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2226

GSHMLSDEQMQIINSLVEAHHKTYDDSYSDFVRFRPPVREGPVTRSASRAASLHSLSDASSDSFNHSPESVDTKLNFSNLLMMYQDSGSPDSSEEDQQSRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLEDMSWSCGGPDFKYCINDVTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMAICLLSPDRPGVQDHVRIEALQDRLCDVLQAYIRIQHPGGRLLYAKMIQKLADLRSLNEEHSKQYRSLSFQPEHSMQLTPLVLEVFGSEVS

Source

organism	Danio rerio
common_name	zebrafish
ncbi_taxonomy_id	7955
host_organism	Escherichia coli BL21

Entity 2 polymer

description	Nuclear receptor coactivator 2
formula_weight	1579.9 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

KHKILHRLLQDSS

Entity 3 non-polymer

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
formula_weight	476.7 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	169

▶

6. Citations (1)

▶

length_a	66.020 Å
length_b	66.020 Å
length_c	262.510 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 65 2 2
int_tables_number	179
crystal_system	hexagonal

resolution	2.100 Å
resolution_low	22.020 Å
r_factor	0.1764
r_work	0.1764
r_free	0.2060

fit	/app/data/saxs_computation/rc/9rcg/9rcg.fit
pddf	/app/data/pr_computation/rc/9rcg/9rcg.pr.out
profile	/app/data/saxs_computation/rc/9rcg/9rcg.dat

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

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)