SAXSdb — 9pxz

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1. Structure Basics

entry_id	9pxz
deposition_date	2025-08-06
title	PRMT5 Bound to Compound 6 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	36.44 Å
rg_electron	36.66 Å
i0	325595000.00
molecular_weight	97478.0 kDa
excluded_volume	94224 Å³
envelope_volume	162720 Å³
shell_volume	40074 Å³
envelope_diameter	130.4 Å
shell_rg	39.27 Å
envelope_rg	36.58 Å
shape_rg	36.63 Å
total_rg	36.83 Å
total_atoms	7384
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	36.90 Å
rg_real_error	1.14 Å
i0_real	3.2560e+08
i0_real_error	5.6560e+06
rg_reciprocal	36.62 Å
i0_reciprocal	325500000.0000
total_estimate	0.7733
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.7 Å
skewness	0.613
kurtosis	-0.306
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	52380000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.654; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.628; Smooth: 0.459

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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	7420

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-1-methyl-N-[(1R)-1-(pyrimidin-2-yl)ethyl]-N-{[5-(trifluoromethyl)pyridin-2-yl]methyl}-1H-pyrazolo[4,3-c]quinoline-8-carboxamide ;
formula_weight	506.5 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	36

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6. Citations (2)

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length_a	103.607 Å
length_b	138.003 Å
length_c	177.955 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	2.470 Å
resolution_low	44.770 Å
r_factor	0.2262
r_work	0.2239
r_free	0.2694

fit	/app/data/saxs_computation/px/9pxz/9pxz.fit
pddf	/app/data/pr_computation/px/9pxz/9pxz.pr.out
profile	/app/data/saxs_computation/px/9pxz/9pxz.dat

PRMT5 Bound to Compound 6 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)