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9qel

Crystal structure of YTHDF2 in complex with compound 4 (AI-DF2-13)

Method: X-RAY DIFFRACTION D_max: 74.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qel
deposition_date	2025-03-10
title	Crystal structure of YTHDF2 in complex with compound 4 (AI-DF2-13)
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	22.04 Å
rg_electron	21.47 Å
i0	20882400.00
molecular_weight	33600.0 kDa
excluded_volume	41472 Å³
envelope_volume	50293 Å³
shell_volume	20076 Å³
envelope_diameter	77.3 Å
shell_rg	27.64 Å
envelope_rg	21.61 Å
shape_rg	21.47 Å
total_rg	22.28 Å
total_atoms	2365
n_residues	297
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	74.1 Å
rg_real	22.08 Å
rg_real_error	0.64 Å
i0_real	2.0880e+07
i0_real_error	2.7590e+05
rg_reciprocal	22.07 Å
i0_reciprocal	20880000.0000
total_estimate	0.7782
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	23.2 Å
skewness	0.409
kurtosis	-0.240
angular_range	— – 0.3600 Å⁻¹
current_alpha	0.0000
highest_alpha	4408000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.743; Stabil: 0.978; Sysdev: 1.000; Positv: 1.000; Valcen: 0.949; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	2520

MGSSYHHHHHHSSGENLYFQHMKHGRVFIIKSYSEDDIHRSIKYNIWCSTEHGNKRLDAAYRSMNGKGPVYLLFSVNGSGHFCGVAEMKSAVDYNTCAGVWSQDKWKGRFDVRWIFVKDVPNSQLRHIRLENNENKPVTNSRDTQEVPLEKAKQVLKIIASYKHTTS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	5

Entity 3 non-polymer

description	6-(METHYLAMINO)-1H-PYRIMIDINE-2,4-DIONE
formula_weight	141.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	98

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6. Citations (2)

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length_a	80.470 Å
length_b	80.470 Å
length_c	113.890 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	1.860 Å
resolution_low	44.100 Å
r_factor	0.2189
r_work	0.2174
r_free	0.2483

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

Crystal structure of YTHDF2 in complex with compound 4 (AI-DF2-13)

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