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9vog

Vitamin D receptor complex with a 5-{4-(m-carboran-1-yl)phenoxy}-4-hydroxypentanoic acid derivative

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

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vog
deposition_date	2025-07-01
last_revision	2025-12-03
title	Vitamin D receptor complex with a 5-{4-(m-carboran-1-yl)phenoxy}-4-hydroxypentanoic acid derivative
keywords	Vitamin D receptor, TRANSCRIPTION; TRANSCRIPTION
method	X-RAY DIFFRACTION

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Download Data

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

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2. SAXS Parameters (CRYSOL)

rg_guinier	19.04 Å
rg_electron	17.99 Å
i0	27063100.00
molecular_weight	27105.0 kDa
excluded_volume	26422 Å³
envelope_volume	41236 Å³
shell_volume	18977 Å³
envelope_diameter	65.6 Å
shell_rg	24.42 Å
envelope_rg	18.34 Å
shape_rg	17.95 Å
total_rg	18.75 Å
total_atoms	2050
n_residues	250
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

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3. P(r) Analysis (GNOM)

dmax	62.3 Å
rg_real	18.94 Å
rg_real_error	0.39 Å
i0_real	2.7060e+07
i0_real_error	3.2720e+05
rg_reciprocal	18.96 Å
i0_reciprocal	27060000.0000
total_estimate	0.8018
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	24.2 Å
skewness	0.221
kurtosis	-0.312
angular_range	— – 0.4200 Å⁻¹
current_alpha	0.0000
highest_alpha	4371000.0000
n_real_points	73
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.809; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Vitamin D3 receptor
formula_weight	30595.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2360

GSHMGSPNSPLKDSLRPKLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMDGSTGSVTLDLSPLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQKLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGNEIS

Source

organism	Rattus norvegicus
common_name	Norway rat
ncbi_taxonomy_id	10116
host_organism	Escherichia coli

Entity 2 polymer

description	Mediator of RNA polymerase II transcription subunit 1
formula_weight	1570.9 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

KNHPMLMNLLKDN

Entity 3 non-polymer

description	;(S)-5-[4-{7-(4-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)phenyl)-1,7-dicarba-closo-dodecaboran-1-yl}phenoxy]-4-hydroxypentanoic acid ;
formula_weight	594.6 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	228

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6. Citations (1)

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length_a	154.680 Å
length_b	42.360 Å
length_c	42.220 Å
angle_alpha	90.00 °
angle_beta	96.16 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	1.430 Å
resolution_low	38.630 Å
r_factor	0.1915
r_work	0.1903
r_free	0.2200

fit	/app/data/saxs_computation/vo/9vog/9vog.fit
pddf	/app/data/pr_computation/vo/9vog/9vog.pr.out
profile	/app/data/saxs_computation/vo/9vog/9vog.dat

Vitamin D receptor complex with a 5-{4-(m-carboran-1-yl)phenoxy}-4-hydroxypentanoic acid derivative

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)