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9v8d

PPARgamma ligand-binding domain in complex with PG08

Method: X-RAY DIFFRACTION D_max: 66.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v8d
deposition_date	2025-05-29
title	PPARgamma ligand-binding domain in complex with PG08
keywords	Nuclear receptor, de novo peptide, 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	20.34 Å
rg_electron	19.06 Å
i0	15927000.00
molecular_weight	31784.0 kDa
excluded_volume	40615 Å³
envelope_volume	47138 Å³
shell_volume	20581 Å³
envelope_diameter	66.7 Å
shell_rg	25.51 Å
envelope_rg	19.28 Å
shape_rg	19.03 Å
total_rg	20.13 Å
total_atoms	2235
n_residues	275
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	66.3 Å
rg_real	20.24 Å
rg_real_error	0.42 Å
i0_real	1.5930e+07
i0_real_error	2.1670e+05
rg_reciprocal	20.26 Å
i0_reciprocal	15930000.0000
total_estimate	0.8104
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.6 Å
skewness	0.204
kurtosis	-0.382
angular_range	— – 0.3900 Å⁻¹
current_alpha	0.0000
highest_alpha	3432000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.845; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Peroxisome proliferator-activated receptor gamma
formula_weight	31449.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2484

QLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	PG08
formula_weight	2637.1 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

YKTANSVXVRHXLLTAILXGVSGSN

Entity 3 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	TRIETHYLENE GLYCOL
formula_weight	150.2 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	205

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6. Citations (1)

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length_a	43.620 Å
length_b	53.460 Å
length_c	66.910 Å
angle_alpha	90.00 °
angle_beta	105.90 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.440 Å
resolution_low	41.986 Å
r_factor	—
r_work	0.1717
r_free	0.2013

fit	/app/data/saxs_computation/v8/9v8d/9v8d.fit
pddf	/app/data/pr_computation/v8/9v8d/9v8d.pr.out
profile	/app/data/saxs_computation/v8/9v8d/9v8d.dat

PPARgamma ligand-binding domain in complex with PG08

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)