SAXSdb — 9py0

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1. Structure Basics

entry_id	9py0
deposition_date	2025-08-06
title	PRMT5 Bound to Compound 12 and MTA
keywords	methyltransferase, inhibitor, TRANSFERASE, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
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	36.41 Å
rg_electron	36.62 Å
i0	325924000.00
molecular_weight	97524.0 kDa
excluded_volume	94266 Å³
envelope_volume	163060 Å³
shell_volume	40192 Å³
envelope_diameter	131.0 Å
shell_rg	39.32 Å
envelope_rg	36.52 Å
shape_rg	36.59 Å
total_rg	36.79 Å
total_atoms	7387
n_residues	926
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	123.8 Å
rg_real	36.87 Å
rg_real_error	1.02 Å
i0_real	3.2590e+08
i0_real_error	5.3750e+06
rg_reciprocal	36.59 Å
i0_reciprocal	325800000.0000
total_estimate	0.7746
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	31.7 Å
skewness	0.611
kurtosis	-0.311
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	51690000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.655; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.628; Smooth: 0.472

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Protein arginine N-methyltransferase 5
formula_weight	73763.6 kDa
ec_number	2.1.1.320
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7425

MDYKDDDDKAAMAVGGAGGSRVSSGRDLNCVPEIADTLGAVAKQGFDFLCMPVFHPRFKREFIQEPAKNRPGPQTRSDLLLSGRDWNTLIVGKLSPWIRPDSKVEKIRRNSEAAMLQELNFGAYLGLPAFLLPLNQEDNTNLARVLTNHIHTGHHSSMFWMRVPLVAPEDLRDDIIENAPTTHTEEYSGEEKTWMWWHNFRTLCDYSKRIAVALEIGADLPSNHVIDRWLGEPIKAAILPTSIFLTNKKGFPVLSKMHQRLIFRLLKLEVQFIITGTNHHSEKEFCSYLQYLEYLSQNRPPPNAYELFAKGYEDYLQSPLQPLMDNLESQTYEVFEKDPIKYSQYQQAIYKCLLDRVPEEEKDTNVQVLMVLGAGRGPLVNASLRAAKQADRRIKLYAVEKNPNAVVTLENWQFEEWGSQVTVVSSDMREWVAPEKADIIVSELLGSFADNELSPECLDGAQHFLKDDGVSIPGEYTSFLAPISSSKLYNEVRACREKDRDPEAQFEMPYVVRLHNFHQLSAPQPCFTFSHPNRDPMIDNNRYCTLEFPVEVNTVLHGFAGYFETVLYQDITLSIRPETHSPGMFSWFPILFPIKQPITVREGQTICVRFWRCSNSKKVWYEWAVTAPVCSAIHNPTGRSYTIGL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Methylosome protein 50
formula_weight	37862.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MHHHHHHHHRKETPPPLVPPAAREWNLPPNAPACMERQLEAARYRSDGALLLGASSLSGRCWAGSLWLFKDPCAAPNEGFCSAGVQTEAGVADLTWVGERGILVASDSGAVELWELDENETLIVSKFCKYEHDDIVSTVSVLSSGTQAVSGSKDICIKVWDLAQQVVLSSYRAHAAQVTCVAASPHKDSVFLSCSEDNRILLWDTRCPKPASQIGCSAPGYLPTSLAWHPQQSEVFVFGDENGTVSLVDTKSTSCVLSSAVHSQCVTGLVFSPHSVPFLASLSEDCSLAVLDSSLSELFRSQAHRDFVRDATWSPLNHSLLTTVGWDHQVVHHVVPTEPLPAPGPASVTE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 3 non-polymer

description	;4-amino-N'-(cyclopropanecarbonyl)-N',1-dimethyl-N-{[5-(trifluoromethyl)pyridin-2-yl]methyl}-1H-pyrazolo[4,3-c]quinoline-8-carbohydrazide ;
formula_weight	497.5 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	5'-DEOXY-5'-METHYLTHIOADENOSINE
formula_weight	297.3 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	35

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6. Citations (2)

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length_a	103.420 Å
length_b	137.669 Å
length_c	178.065 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	I 2 2 2
int_tables_number	23
crystal_system	orthorhombic

resolution	2.360 Å
resolution_low	41.340 Å
r_factor	0.2328
r_work	0.2300
r_free	0.2830

fit	/app/data/saxs_computation/py/9py0/9py0.fit
pddf	/app/data/pr_computation/py/9py0/9py0.pr.out
profile	/app/data/saxs_computation/py/9py0/9py0.dat

PRMT5 Bound to Compound 12 and MTA

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 (2)

7. Files & Curves (10)

Files (7)

Curves (3)