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9rs3

Crystal structure of the human METTL3-METTL14 in complex with compound 3

Method: X-RAY DIFFRACTION D_max: 83.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rs3
deposition_date	2025-06-30
title	Crystal structure of the human METTL3-METTL14 in complex with compound 3
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	24.42 Å
rg_electron	23.94 Å
i0	76211100.00
molecular_weight	46180.0 kDa
excluded_volume	44883 Å³
envelope_volume	73356 Å³
shell_volume	26172 Å³
envelope_diameter	86.0 Å
shell_rg	30.57 Å
envelope_rg	24.14 Å
shape_rg	23.96 Å
total_rg	24.48 Å
total_atoms	3497
n_residues	445
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	83.0 Å
rg_real	24.50 Å
rg_real_error	0.69 Å
i0_real	7.6210e+07
i0_real_error	1.1320e+06
rg_reciprocal	24.49 Å
i0_reciprocal	76210000.0000
total_estimate	0.8612
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.4 Å
skewness	0.487
kurtosis	-0.134
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	15490000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.768; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.922; Smooth: 0.969

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

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	3589

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	S-ADENOSYL-L-HOMOCYSTEINE
formula_weight	384.4 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	4-[[[4-[(4,4-dimethylpiperidin-1-yl)methyl]-2-oxidanyl-phenyl]amino]methyl]-1-(4-phenylmethoxypyridin-2-yl)piperidin-4-ol
formula_weight	530.7 kDa
src_method	nat
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	89

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6. Citations (1)

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length_a	63.940 Å
length_b	63.940 Å
length_c	226.850 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	2.110 Å
resolution_low	44.680 Å
r_factor	0.2030
r_work	0.2013
r_free	0.2353

fit	/app/data/saxs_computation/rs/9rs3/9rs3.fit
pddf	/app/data/pr_computation/rs/9rs3/9rs3.pr.out
profile	/app/data/saxs_computation/rs/9rs3/9rs3.dat

Crystal structure of the human METTL3-METTL14 in complex with compound 3

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 (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)