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9rry

Crystal structure of the human METTL3-METTL14 in complex with compound 1 (AD-79)

Method: X-RAY DIFFRACTION D_max: 84.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rry
deposition_date	2025-06-30
title	Crystal structure of the human METTL3-METTL14 in complex with compound 1 (AD-79)
keywords	METTL3, inhibitor, complex, m6A, TRANSFERASE; TRANSFERASE
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	24.14 Å
rg_electron	23.64 Å
i0	70880700.00
molecular_weight	44647.0 kDa
excluded_volume	43496 Å³
envelope_volume	70416 Å³
shell_volume	25558 Å³
envelope_diameter	86.3 Å
shell_rg	30.24 Å
envelope_rg	23.79 Å
shape_rg	23.65 Å
total_rg	24.19 Å
total_atoms	3387
n_residues	435
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	84.8 Å
rg_real	24.23 Å
rg_real_error	0.65 Å
i0_real	7.0880e+07
i0_real_error	9.6780e+05
rg_reciprocal	24.21 Å
i0_reciprocal	70880000.0000
total_estimate	0.8448
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.5 Å
skewness	0.511
kurtosis	-0.092
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	15500000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.709; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.894; Smooth: 0.956

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	N6-adenosine-methyltransferase catalytic subunit
formula_weight	26017.8 kDa
ec_number	2.1.1.348
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3497

MALTQSVGGDSSADRLFPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKPKNL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	N(6)-adenosine-methyltransferase non-catalytic subunit METTL14
formula_weight	35690.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MHHHHHHSSGRENLYFQGLKGTQSLNPHNDYCQHFVDTGHRPQNFIRDVGLADRFEEYPKLRELIRLKDELIAKSNTPPMYLQADIEAFDIRELTPKFDVILLEPPLEEYYRETGITANEKCWTWDDIMKLEIDEIAAPRSFIFLWCGSGEGLDLGRVCLRKWGYRRCEDICWIKTNKNNPGKTKTLDPKAVFQRTKEHCLMGIKGTVKRSTDGDFIHANVDIDLIITEEPEIGNIEKPVEIFHIIEHFCLGRRRLHLFGRDSTIRPGWLTVGPTLTNSNYNAETYASYFSAPNSYLTGCTEEIERL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 3 non-polymer

description	8-[4-[(4,4-dimethylpiperidin-1-yl)methyl]phenyl]-2-[6-(methylamino)pyrimidin-4-yl]-2,5,8-triazaspiro[3.5]nonan-6-one
formula_weight	449.6 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	107

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6. Citations (1)

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length_a	63.980 Å
length_b	63.980 Å
length_c	226.180 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 32 2 1
int_tables_number	154
crystal_system	trigonal

resolution	1.910 Å
resolution_low	44.650 Å
r_factor	0.2226
r_work	0.2212
r_free	0.2508

fit	/app/data/saxs_computation/rr/9rry/9rry.fit
pddf	/app/data/pr_computation/rr/9rry/9rry.pr.out
profile	/app/data/saxs_computation/rr/9rry/9rry.dat

Crystal structure of the human METTL3-METTL14 in complex with compound 1 (AD-79)

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

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)