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9s9m

Crystal structure of p53 cancer mutant Y220C in complex with rezatapopt analog 7

Method: X-RAY DIFFRACTION D_max: 74.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s9m
deposition_date	2025-08-06
title	Crystal structure of p53 cancer mutant Y220C in complex with rezatapopt analog 7
keywords	p53, tumor suppressor, protein stability, protein unfolding disease, small-molecule stabilizer, 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	24.11 Å
rg_electron	23.38 Å
i0	67926000.00
molecular_weight	41685.0 kDa
excluded_volume	39458 Å³
envelope_volume	67805 Å³
shell_volume	24306 Å³
envelope_diameter	77.5 Å
shell_rg	30.19 Å
envelope_rg	23.17 Å
shape_rg	23.37 Å
total_rg	23.98 Å
total_atoms	3115
n_residues	395
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	74.8 Å
rg_real	24.03 Å
rg_real_error	0.39 Å
i0_real	6.7930e+07
i0_real_error	8.8690e+05
rg_reciprocal	24.05 Å
i0_reciprocal	67930000.0000
total_estimate	0.9142
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	28.0 Å
skewness	0.198
kurtosis	-0.583
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	5941000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.962; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.995

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Cellular tumor antigen p53
formula_weight	24530.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3482

SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKLFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRAEYLDDRNTFRHSVVVPCEPPEVGSDCTTIHYNYMCYSSCMGGMNRRPILTIITLEDSSGNLLGRDSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNT

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	2-[3-[(4-dimethylphosphorylphenyl)amino]prop-1-ynyl]-~{N}-(1-methylpiperidin-4-yl)-1-[2,2,2-tris(fluoranyl)ethyl]indol-4-amine
formula_weight	516.5 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	286

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6. Citations (1)

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length_a	64.832 Å
length_b	71.037 Å
length_c	104.564 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	1.830 Å
resolution_low	55.100 Å
r_factor	0.1932
r_work	0.1916
r_free	0.2255

fit	/app/data/saxs_computation/s9/9s9m/9s9m.fit
pddf	/app/data/pr_computation/s9/9s9m/9s9m.pr.out
profile	/app/data/saxs_computation/s9/9s9m/9s9m.dat