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9s9q

Crystal structure of p53 cancer mutant Y220N in complex with rezatapopt

Method: X-RAY DIFFRACTION D_max: 74.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s9q
deposition_date	2025-08-06
title	Crystal structure of p53 cancer mutant Y220N in complex with rezatapopt
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	24.22 Å
rg_electron	23.49 Å
i0	70103900.00
molecular_weight	42307.0 kDa
excluded_volume	40004 Å³
envelope_volume	68885 Å³
shell_volume	24456 Å³
envelope_diameter	77.3 Å
shell_rg	30.31 Å
envelope_rg	23.35 Å
shape_rg	23.48 Å
total_rg	24.07 Å
total_atoms	3164
n_residues	396
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	74.4 Å
rg_real	24.13 Å
rg_real_error	0.52 Å
i0_real	7.0100e+07
i0_real_error	1.0180e+06
rg_reciprocal	24.16 Å
i0_reciprocal	70100000.0000
total_estimate	0.9140
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	27.9 Å
skewness	0.197
kurtosis	-0.589
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	6002000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.968; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.977

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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	24541.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3573

SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKLFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRAEYLDDRNTFRHSVVVPNEPPEVGSDCTTIHYNYMCYSSCMGGMNRRPILTIITLEDSSGNLLGRDSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNT

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	;4-[3-[4-[[(3~{S},4~{R})-3-fluoranyl-1-methyl-piperidin-4-yl]amino]-1-[2,2,2-tris(fluoranyl)ethyl]indol-2-yl]prop-2-ynylamino]-3-methoxy-~{N}-methyl-benzamide ;
formula_weight	545.6 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	8

Entity 5 non-polymer

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

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	355

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6. Citations (1)

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length_a	65.075 Å
length_b	71.150 Å
length_c	104.597 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	1.870 Å
resolution_low	48.000 Å
r_factor	0.1985
r_work	0.1962
r_free	0.2425

fit	/app/data/saxs_computation/s9/9s9q/9s9q.fit
pddf	/app/data/pr_computation/s9/9s9q/9s9q.pr.out
profile	/app/data/saxs_computation/s9/9s9q/9s9q.dat