← Back to search

9vzt

X-ray structure of human PPARalpha ligand binding domain-10-oxostearic acid (10-oxoSA) co-crystals obtained by cross-seeding

Method: X-RAY DIFFRACTION D_max: 65.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9vzt
deposition_date	2025-07-23
last_revision	2026-05-27
title	X-ray structure of human PPARalpha ligand binding domain-10-oxostearic acid (10-oxoSA) co-crystals obtained by cross-seeding
keywords	Nuclear receptor, Protein-ligand complex, PPAR, Transcription; TRANSCRIPTION
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	20.12 Å
rg_electron	18.91 Å
i0	15038100.00
molecular_weight	30374.0 kDa
excluded_volume	38609 Å³
envelope_volume	44371 Å³
shell_volume	19689 Å³
envelope_diameter	68.2 Å
shell_rg	25.30 Å
envelope_rg	19.19 Å
shape_rg	18.91 Å
total_rg	19.88 Å
total_atoms	2169
n_residues	265
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	65.9 Å
rg_real	20.06 Å
rg_real_error	0.39 Å
i0_real	1.5040e+07
i0_real_error	1.9870e+05
rg_reciprocal	20.07 Å
i0_reciprocal	15040000.0000
total_estimate	0.8064
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	25.4 Å
skewness	0.278
kurtosis	-0.311
angular_range	— – 0.3950 Å⁻¹
current_alpha	0.0000
highest_alpha	3537000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.827; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	Peroxisome proliferator-activated receptor alpha
formula_weight	30856.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2418

GSHMTADLKSLAKRIYEAYLKNFNMNKVKARVILSGKASNNPPFVIHDMETLCMAEKTLVAKLVANGIQNKEAEVRIFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITREFLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQLVTEHAQLVQIIKKTESDAALHPLLQEIYRDMY

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	10-oxooctadecanoic acid
formula_weight	298.5 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	133

▶

6. Citations (1)

▶

length_a	44.596 Å
length_b	61.498 Å
length_c	53.001 Å
angle_alpha	90.00 °
angle_beta	106.66 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.475 Å
resolution_low	30.749 Å
r_factor	0.1887
r_work	0.1880
r_free	0.2019

fit	/app/data/saxs_computation/vz/9vzt/9vzt.fit
pddf	/app/data/pr_computation/vz/9vzt/9vzt.pr.out
profile	/app/data/saxs_computation/vz/9vzt/9vzt.dat

X-ray structure of human PPARalpha ligand binding domain-10-oxostearic acid (10-oxoSA) co-crystals obtained by cross-seeding

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