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9qfi

Crystal structure of YTHDF2 in complex with compound 6 (AI-DF2-47)

Method: X-RAY DIFFRACTION D_max: 73.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qfi
deposition_date	2025-03-11
last_revision	2025-12-03
title	Crystal structure of YTHDF2 in complex with compound 6 (AI-DF2-47)
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	22.56 Å
rg_electron	21.68 Å
i0	36695900.00
molecular_weight	30934.0 kDa
excluded_volume	29729 Å³
envelope_volume	49453 Å³
shell_volume	19904 Å³
envelope_diameter	76.0 Å
shell_rg	27.30 Å
envelope_rg	21.60 Å
shape_rg	21.58 Å
total_rg	22.37 Å
total_atoms	2333
n_residues	295
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	73.5 Å
rg_real	22.58 Å
rg_real_error	0.46 Å
i0_real	3.6700e+07
i0_real_error	5.0830e+05
rg_reciprocal	22.58 Å
i0_reciprocal	36700000.0000
total_estimate	0.8931
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.4 Å
skewness	0.327
kurtosis	-0.539
angular_range	— – 0.3500 Å⁻¹
current_alpha	0.0000
highest_alpha	6364000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.976

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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	2432

MGSSYHHHHHHSSGENLYFQHMKHGRVFIIKSYSEDDIHRSIKYNIWCSTEHGNKRLDAAYRSMNGKGPVYLLFSVNGSGHFCGVAEMKSAVDYNTCAGVWSQDKWKGRFDVRWIFVKDVPNSQLRHIRLENNENKPVTNSRDTQEVPLEKAKQVLKIIASYKHTTS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	3-methyl-1~{H}-pyrazolo[3,4-d]pyrimidin-4-amine
formula_weight	149.2 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	83

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6. Citations (2)

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length_a	79.140 Å
length_b	79.140 Å
length_c	110.270 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	1.910 Å
resolution_low	42.960 Å
r_factor	0.2260
r_work	0.2243
r_free	0.2559

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