SAXSdb — 9wkw

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1. Structure Basics

entry_id	9wkw
deposition_date	2025-09-01
last_revision	2026-04-29
title	Wild-type Menin complexed with DS-1594
keywords	HUMAN MENIN, TRANSCRIPTION, M322I MUTANT INHIBITOR COMPLEX, SNDX-5613; 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	31.72 Å
rg_electron	30.81 Å
i0	165574000.00
molecular_weight	104450.0 kDa
excluded_volume	131630 Å³
envelope_volume	166240 Å³
shell_volume	43890 Å³
envelope_diameter	105.1 Å
shell_rg	38.88 Å
envelope_rg	30.14 Å
shape_rg	30.77 Å
total_rg	31.65 Å
total_atoms	7364
n_residues	911
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	97.4 Å
rg_real	31.52 Å
rg_real_error	0.53 Å
i0_real	1.6560e+08
i0_real_error	2.4920e+06
rg_reciprocal	31.61 Å
i0_reciprocal	165600000.0000
total_estimate	0.9030
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	44.8 Å
skewness	0.095
kurtosis	-0.527
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	54300000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.953

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Menin
formula_weight	54723.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	8218

GLKTAQKTLFPLRSIDDVVRLFAAELGREEPDLVLLSLVLGFVEHFLAVNRVIPTNVPELTFQPSPAPDPPGGLTYFPVADLSIIAALYARFTAQIRGAVDLSLYPREGGVSSRELVKKVSDVIWNSLSRSYFKDRAHIQSLFSFITGTKLDSSGVAFAVVGACQALGLRDVHLALSEDHAWVVFGPNGEQTAEVTWHGKGNEDRRGQTVNAGVAERSWLYLKGSYMRCDRKMEVAFMVCAINPSIDLHTDSLELLQLQQKLLWLLYDLGHLERYPMALGNLADLEELEPTPGRPDPLTLYHKGIASAKTYYRDEHIYPYMYLAGYHCRNRNVREALQAWADTATVIQDYNYCREDEEIYKEFFEVANDVIPNLLKEAASLLEAGEERPGEQSQGTQSQGSALQDPECFAHLLRFYDGICKWEEGSPTPVLHVGWATFLVQSLGRFEGQVRQKVRITFQSEKMKGMKELLVATKINSSAIKLQLTAQS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	;(1R,2S,4R)-4-[[4-(5,6-dimethoxypyridazin-3-yl)phenyl]methylamino]-2-[methyl-[6-[2,2,2-tris(fluoranyl)ethyl]thieno[2,3-d]pyrimidin-4-yl]amino]cyclopentan-1-ol ;
formula_weight	574.6 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	15

Entity 4 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	nat
entity_count	2

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	nat
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	682

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6. Citations (1)

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length_a	69.786 Å
length_b	78.646 Å
length_c	92.615 Å
angle_alpha	90.00 °
angle_beta	101.51 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.630 Å
resolution_low	48.120 Å
r_factor	0.1549
r_work	0.1538
r_free	0.1763

fit	/app/data/saxs_computation/wk/9wkw/9wkw.fit
pddf	/app/data/pr_computation/wk/9wkw/9wkw.pr.out
profile	/app/data/saxs_computation/wk/9wkw/9wkw.dat

Wild-type Menin complexed with DS-1594

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