SAXSdb — 9wna

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1. Structure Basics

entry_id	9wna
deposition_date	2025-09-04
title	[M322I] Menin complexed with DSP-5336
keywords	HUMAN MENIN, TRANSCRIPTION, M322I MUTANT INHIBITOR COMPLEX, DS1594; 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	31.85 Å
rg_electron	31.30 Å
i0	323272000.00
molecular_weight	97180.0 kDa
excluded_volume	94424 Å³
envelope_volume	165840 Å³
shell_volume	44128 Å³
envelope_diameter	114.9 Å
shell_rg	38.42 Å
envelope_rg	30.94 Å
shape_rg	31.30 Å
total_rg	31.72 Å
total_atoms	7382
n_residues	924
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	108.0 Å
rg_real	31.85 Å
rg_real_error	0.87 Å
i0_real	3.2330e+08
i0_real_error	5.0030e+06
rg_reciprocal	31.85 Å
i0_reciprocal	323300000.0000
total_estimate	0.8784
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	36.7 Å
skewness	0.385
kurtosis	-0.209
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	43950000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.945

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Menin
formula_weight	54705.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7845

GLKTAQKTLFPLRSIDDVVRLFAAELGREEPDLVLLSLVLGFVEHFLAVNRVIPTNVPELTFQPSPAPDPPGGLTYFPVADLSIIAALYARFTAQIRGAVDLSLYPREGGVSSRELVKKVSDVIWNSLSRSYFKDRAHIQSLFSFITGTKLDSSGVAFAVVGACQALGLRDVHLALSEDHAWVVFGPNGEQTAEVTWHGKGNEDRRGQTVNAGVAERSWLYLKGSYMRCDRKMEVAFMVCAINPSIDLHTDSLELLQLQQKLLWLLYDLGHLERYPMALGNLADLEELEPTPGRPDPLTLYHKGIASAKTYYRDEHIYPYIYLAGYHCRNRNVREALQAWADTATVIQDYNYCREDEEIYKEFFEVANDVIPNLLKEAASLLEAGEERPGEQSQGTQSQGSALQDPECFAHLLRFYDGICKWEEGSPTPVLHVGWATFLVQSLGRFEGQVRQKVRITFQSEKMKGMKELLVATKINSSAIKLQLTAQS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	;5-fluoro-2-[(4-{7-[(1S,3S,4R)-5-methylidene-2-azabicyclo[2.2.2]octane-3-carbonyl]-2,7-diazaspiro[3.5]nonan-2-yl}pyrimidin-5-yl)oxy]-N,N-di(propan-2-yl)benzamide ;
formula_weight	590.7 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	4

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	358

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6. Citations (1)

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length_a	58.701 Å
length_b	86.058 Å
length_c	201.892 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	—

resolution	2.000 Å
resolution_low	48.540 Å
r_factor	0.1747
r_work	0.1728
r_free	0.2124

fit	/app/data/saxs_computation/wn/9wna/9wna.fit
pddf	/app/data/pr_computation/wn/9wna/9wna.pr.out
profile	/app/data/saxs_computation/wn/9wna/9wna.dat

[M322I] Menin complexed with DSP-5336

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