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9vpq

Crystal structure of METTL9 in complex with compound 15k

Method: X-RAY DIFFRACTION D_max: 89.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vpq
deposition_date	2025-07-03
title	Crystal structure of METTL9 in complex with compound 15k
keywords	Protein-L-histidine N-pros-methyltransferase, Inhibitor, Complex, 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	27.41 Å
rg_electron	26.95 Å
i0	100624000.00
molecular_weight	53966.0 kDa
excluded_volume	52825 Å³
envelope_volume	86916 Å³
shell_volume	27643 Å³
envelope_diameter	92.1 Å
shell_rg	33.18 Å
envelope_rg	26.89 Å
shape_rg	26.96 Å
total_rg	27.42 Å
total_atoms	4124
n_residues	532
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	89.1 Å
rg_real	27.51 Å
rg_real_error	0.61 Å
i0_real	1.0060e+08
i0_real_error	1.3700e+06
rg_reciprocal	27.48 Å
i0_reciprocal	100600000.0000
total_estimate	0.8834
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.6 Å
skewness	0.415
kurtosis	-0.415
angular_range	— – 0.2900 Å⁻¹
current_alpha	0.0000
highest_alpha	9295000.0000
n_real_points	59
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.872

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Protein-L-histidine N-pros-methyltransferase
formula_weight	31371.7 kDa
ec_number	2.1.1.-
mutation	L95A, F96A, L99A, F103A, V107A, F111A
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4243

SAAGGRKENHQWYVCNREKLCESLQAVFVQSYLDQGTQIFLNNSIEKSGWAAIQAYHSAVSSAFSLAMSRTSINGLLGRGSMFVFSPDQFQRLLKINPDWKTHRLLDLGAGDGEVTKIMSPHFEEIYATELSETMIWQLQKKKYRVLGINEWQNTGFQYDVISCLNLLDRCDQPLTLLKDIRSVLEPTRGRVILALVLPFHPYVENVGGKWEKPSEILEIKGQNWEEQVNSLPEVFRKAGFVIEAFTRLPYLCEGDMYNDYYVLDDAVFVLKPV

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Zinc transporter ZIP5
formula_weight	1199.2 kDa
src_method	syn
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D

GHQGHSHGHQGG

Entity 3 non-polymer

description	~{N}-[2-fluoranyl-5-[8-fluoranyl-4-[(3-hydroxyphenyl)amino]quinazolin-6-yl]pyridin-3-yl]benzenesulfonamide
formula_weight	505.5 kDa
src_method	nat
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	119

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6. Citations (1)

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length_a	142.394 Å
length_b	45.651 Å
length_c	106.895 Å
angle_alpha	90.00 °
angle_beta	123.23 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	2.280 Å
resolution_low	35.570 Å
r_factor	0.2235
r_work	0.2193
r_free	0.2730

fit	/app/data/saxs_computation/vp/9vpq/9vpq.fit
pddf	/app/data/pr_computation/vp/9vpq/9vpq.pr.out
profile	/app/data/saxs_computation/vp/9vpq/9vpq.dat

Crystal structure of METTL9 in complex with compound 15k

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)