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9yks

Crystal structure of the G9a (EHMT2) SET domain in complex with SAM and TNG917

Method: X-RAY DIFFRACTION D_max: 117.1 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yks
deposition_date	2025-10-07
title	Crystal structure of the G9a (EHMT2) SET domain in complex with SAM and TNG917
keywords	methyltransferase, SAM, histone, 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	37.46 Å
rg_electron	36.97 Å
i0	543164000.00
molecular_weight	122490.0 kDa
excluded_volume	116230 Å³
envelope_volume	220770 Å³
shell_volume	50067 Å³
envelope_diameter	126.8 Å
shell_rg	43.11 Å
envelope_rg	36.28 Å
shape_rg	36.97 Å
total_rg	37.26 Å
total_atoms	9124
n_residues	1095
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	117.1 Å
rg_real	37.35 Å
rg_real_error	0.69 Å
i0_real	5.4320e+08
i0_real_error	8.7720e+06
rg_reciprocal	37.42 Å
i0_reciprocal	543200000.0000
total_estimate	0.9114
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	44.6 Å
skewness	0.152
kurtosis	-0.657
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0001
highest_alpha	22880000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.968; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.941

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Histone-lysine N-methyltransferase EHMT2
formula_weight	32517.8 kDa
ec_number	2.1.1.-,2.1.1.367
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	10403

GNRAIRTEKIICRDVARGYENVPIPCVNGVDGEPCPEDYKYISENCETSTMNIDRNITHLQHCTCVDDCSSSNCLCGQLSIRCWYDKDGRLLQEFNKIEPPLIFECNQACSCWRNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVREDDSYLFDLDNKDGEVYCIDARYYGNISRFINHLCDPNIIPVRVFMLHQDLRFPRIAFFSSRDIRTGEELGFDYGDRFWDIKSKYFTCQCGSEKCKHSAEAIALEQSRLARLD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	16

Entity 3 non-polymer

description	S-ADENOSYLMETHIONINE
formula_weight	398.4 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	N~2~-[(7M)-6-fluoro-7-(2,5,6,7-tetrahydro-1H-azepin-4-yl)-2,3-dihydro-1-benzofuran-5-yl]-N~4~,6-dimethylpyrimidine-2,4-diamine
formula_weight	369.4 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	13

Entity 6 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1029

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6. Citations (1)

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length_a	56.600 Å
length_b	76.980 Å
length_c	134.140 Å
angle_alpha	90.00 °
angle_beta	89.80 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.790 Å
resolution_low	45.600 Å
r_factor	0.1948
r_work	0.1919
r_free	0.2516

fit	/app/data/saxs_computation/yk/9yks/9yks.fit
pddf	/app/data/pr_computation/yk/9yks/9yks.pr.out
profile	/app/data/saxs_computation/yk/9yks/9yks.dat