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9s9l

Crystal structure of p53 cancer mutant Y220C in complex with rezatapopt precursor

Method: X-RAY DIFFRACTION D_max: 74.3 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s9l
deposition_date	2025-08-06
title	Crystal structure of p53 cancer mutant Y220C in complex with rezatapopt precursor
keywords	p53, tumor suppressor, protein stability, protein unfolding disease, small-molecule stabilizer, cancer therapy, 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	23.95 Å
rg_electron	23.24 Å
i0	67977900.00
molecular_weight	41647.0 kDa
excluded_volume	39430 Å³
envelope_volume	67625 Å³
shell_volume	24378 Å³
envelope_diameter	77.1 Å
shell_rg	29.94 Å
envelope_rg	23.05 Å
shape_rg	23.23 Å
total_rg	23.82 Å
total_atoms	3116
n_residues	397
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	74.3 Å
rg_real	23.88 Å
rg_real_error	0.45 Å
i0_real	6.7980e+07
i0_real_error	9.2010e+05
rg_reciprocal	23.90 Å
i0_reciprocal	67980000.0000
total_estimate	0.9134
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	27.9 Å
skewness	0.210
kurtosis	-0.567
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	6376000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.959; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.996

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

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	3726

SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKLFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRAEYLDDRNTFRHSVVVPCEPPEVGSDCTTIHYNYMCYSSCMGGMNRRPILTIITLEDSSGNLLGRDSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNT

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	~{N}-[3-[1-ethyl-5-(methylaminomethyl)indol-2-yl]prop-2-ynyl]aniline
formula_weight	317.4 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

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

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	515

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6. Citations (1)

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length_a	64.766 Å
length_b	71.245 Å
length_c	104.588 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	1.380 Å
resolution_low	47.900 Å
r_factor	0.1497
r_work	0.1484
r_free	0.1742

fit	/app/data/saxs_computation/s9/9s9l/9s9l.fit
pddf	/app/data/pr_computation/s9/9s9l/9s9l.pr.out
profile	/app/data/saxs_computation/s9/9s9l/9s9l.dat