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9qfl

Crystal structure of YTHDF2 in complex with compound 15 (AI-DF2-68)

Method: X-RAY DIFFRACTION D_max: 75.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qfl
deposition_date	2025-03-11
title	Crystal structure of YTHDF2 in complex with compound 15 (AI-DF2-68)
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	22.02 Å
rg_electron	21.48 Å
i0	38223100.00
molecular_weight	31686.0 kDa
excluded_volume	30453 Å³
envelope_volume	50629 Å³
shell_volume	20224 Å³
envelope_diameter	79.5 Å
shell_rg	27.67 Å
envelope_rg	21.66 Å
shape_rg	21.50 Å
total_rg	22.06 Å
total_atoms	2392
n_residues	299
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	75.0 Å
rg_real	22.05 Å
rg_real_error	0.54 Å
i0_real	3.8220e+07
i0_real_error	5.0310e+05
rg_reciprocal	22.05 Å
i0_reciprocal	38220000.0000
total_estimate	0.7922
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	24.6 Å
skewness	0.406
kurtosis	-0.256
angular_range	— – 0.3600 Å⁻¹
current_alpha	0.0000
highest_alpha	6188000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.794; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.917; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

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	2577

MGSSYHHHHHHSSGENLYFQHMKHGRVFIIKSYSEDDIHRSIKYNIWCSTEHGNKRLDAAYRSMNGKGPVYLLFSVNGSGHFCGVAEMKSAVDYNTCAGVWSQDKWKGRFDVRWIFVKDVPNSQLRHIRLENNENKPVTNSRDTQEVPLEKAKQVLKIIASYKHTTS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	6-sulfanylidene-1,7-dihydropyrazolo[3,4-d]pyrimidin-4-one
formula_weight	168.2 kDa
src_method	syn
entity_count	1

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	4

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	148

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6. Citations (2)

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length_a	79.720 Å
length_b	79.720 Å
length_c	114.430 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	1.700 Å
resolution_low	39.860 Å
r_factor	0.2043
r_work	0.2034
r_free	0.2227

fit	/app/data/saxs_computation/qf/9qfl/9qfl.fit
pddf	/app/data/pr_computation/qf/9qfl/9qfl.pr.out
profile	/app/data/saxs_computation/qf/9qfl/9qfl.dat