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9qem

Crystal structure of YTHDF2 in complex with compound 3 (AI-DF2-11)

Method: X-RAY DIFFRACTION D_max: 74.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qem
deposition_date	2025-03-10
title	Crystal structure of YTHDF2 in complex with compound 3 (AI-DF2-11)
keywords	Inhibitor, m6A reader, RNA BINDING PROTEIN; RNA BINDING PROTEIN
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	22.99 Å
rg_electron	22.12 Å
i0	35713400.00
molecular_weight	30497.0 kDa
excluded_volume	29252 Å³
envelope_volume	49463 Å³
shell_volume	19492 Å³
envelope_diameter	76.2 Å
shell_rg	27.65 Å
envelope_rg	21.93 Å
shape_rg	22.03 Å
total_rg	22.79 Å
total_atoms	2295
n_residues	288
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	74.7 Å
rg_real	23.01 Å
rg_real_error	0.51 Å
i0_real	3.5710e+07
i0_real_error	4.8900e+05
rg_reciprocal	23.01 Å
i0_reciprocal	35710000.0000
total_estimate	0.8928
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	21.8 Å
skewness	0.291
kurtosis	-0.604
angular_range	— – 0.3450 Å⁻¹
current_alpha	0.0000
highest_alpha	6476000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.944; Smooth: 0.968

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	YTH domain-containing family protein 2
formula_weight	19367.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	2342

MGSSYHHHHHHSSGENLYFQHMKHGRVFIIKSYSEDDIHRSIKYNIWCSTEHGNKRLDAAYRSMNGKGPVYLLFSVNGSGHFCGVAEMKSAVDYNTCAGVWSQDKWKGRFDVRWIFVKDVPNSQLRHIRLENNENKPVTNSRDTQEVPLEKAKQVLKIIASYKHTTS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	5-[[(3-methoxyphenyl)amino]methylidene]-2-sulfanylidene-1,3-diazinane-4,6-dione
formula_weight	277.3 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	5

Entity 5 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	31

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6. Citations (2)

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length_a	80.060 Å
length_b	80.060 Å
length_c	110.800 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 65
int_tables_number	170
crystal_system	hexagonal

resolution	2.260 Å
resolution_low	43.280 Å
r_factor	0.2207
r_work	0.2186
r_free	0.2598

fit	/app/data/saxs_computation/qe/9qem/9qem.fit
pddf	/app/data/pr_computation/qe/9qem/9qem.pr.out
profile	/app/data/saxs_computation/qe/9qem/9qem.dat