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9spp

p53 cancer mutant Y234C in complex with DARPin C10

Method: X-RAY DIFFRACTION D_max: 70.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9spp
deposition_date	2025-09-17
last_revision	2026-04-22
title	p53 cancer mutant Y234C in complex with DARPin C10
keywords	;p53, tumor suppressor, cancer mutation, protein stability, protein unfolding disease, designed ankyrin repeat proteins, thermostabilization, mutant p53 reactivation, 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	21.59 Å
rg_electron	20.64 Å
i0	23155600.00
molecular_weight	35121.0 kDa
excluded_volume	43360 Å³
envelope_volume	51567 Å³
shell_volume	21159 Å³
envelope_diameter	73.8 Å
shell_rg	26.92 Å
envelope_rg	20.79 Å
shape_rg	20.61 Å
total_rg	21.53 Å
total_atoms	2455
n_residues	320
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	70.7 Å
rg_real	21.58 Å
rg_real_error	0.50 Å
i0_real	2.3160e+07
i0_real_error	3.0700e+05
rg_reciprocal	21.59 Å
i0_reciprocal	23160000.0000
total_estimate	0.8085
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	24.9 Å
skewness	0.361
kurtosis	-0.306
angular_range	— – 0.3700 Å⁻¹
current_alpha	0.0000
highest_alpha	5237000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.000

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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	22661.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2860

SSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHCNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	DARPin C10
formula_weight	13527.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

GSDLGKKLLEAAWHGQDDEVRILMANGADVNATDQSGMTPLHLAAWRGHLEIVEVLLKTGADVNAIDRWGKTPLHLAARIGHLEIVEVLLKAGADVNAQDKFGKTPFDLAIDNGNEDIAEVLQKAA

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	8

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	342

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6. Citations (1)

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length_a	37.737 Å
length_b	93.773 Å
length_c	53.223 Å
angle_alpha	90.00 °
angle_beta	110.20 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.470 Å
resolution_low	46.900 Å
r_factor	0.1574
r_work	0.1556
r_free	0.1921

fit	/app/data/saxs_computation/sp/9spp/9spp.fit
pddf	/app/data/pr_computation/sp/9spp/9spp.pr.out
profile	/app/data/saxs_computation/sp/9spp/9spp.dat

p53 cancer mutant Y234C in complex with DARPin C10

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)