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9qeo

Crystal structure of YTHDF2 in complex with compound 5 (AI-DF2-36)

Method: X-RAY DIFFRACTION D_max: 77.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qeo
deposition_date	2025-03-10
title	Crystal structure of YTHDF2 in complex with compound 5 (AI-DF2-36)
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	22.12 Å
rg_electron	21.60 Å
i0	40131700.00
molecular_weight	32173.0 kDa
excluded_volume	30751 Å³
envelope_volume	51909 Å³
shell_volume	20583 Å³
envelope_diameter	79.6 Å
shell_rg	27.73 Å
envelope_rg	21.82 Å
shape_rg	21.60 Å
total_rg	22.17 Å
total_atoms	2421
n_residues	300
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	77.8 Å
rg_real	22.16 Å
rg_real_error	0.59 Å
i0_real	4.0130e+07
i0_real_error	6.0230e+05
rg_reciprocal	22.15 Å
i0_reciprocal	40130000.0000
total_estimate	0.8521
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.4 Å
skewness	0.416
kurtosis	-0.235
angular_range	— – 0.3600 Å⁻¹
current_alpha	0.0000
highest_alpha	7368000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.754; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.878; Smooth: 0.935

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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	2594

MGSSYHHHHHHSSGENLYFQHMKHGRVFIIKSYSEDDIHRSIKYNIWCSTEHGNKRLDAAYRSMNGKGPVYLLFSVNGSGHFCGVAEMKSAVDYNTCAGVWSQDKWKGRFDVRWIFVKDVPNSQLRHIRLENNENKPVTNSRDTQEVPLEKAKQVLKIIASYKHTTS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	2-(methylamino)pyridine-3-carboxamide
formula_weight	151.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	6

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	134

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6. Citations (2)

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length_a	80.560 Å
length_b	80.560 Å
length_c	114.370 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	1.980 Å
resolution_low	40.280 Å
r_factor	0.2146
r_work	0.2122
r_free	0.2580

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