SAXSdb — 9t43

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1. Structure Basics

entry_id	9t43
deposition_date	2025-10-30
title	Human PRMT5:MEP50 in complex with AZD3470
keywords	PRMT5, MEP50, clinical candidate, AZD3470, cancer, oncology, inhibitor, MTAP deletion, MTA, 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	36.53 Å
rg_electron	36.81 Å
i0	319076000.00
molecular_weight	96453.0 kDa
excluded_volume	93249 Å³
envelope_volume	161680 Å³
shell_volume	39827 Å³
envelope_diameter	133.5 Å
shell_rg	39.16 Å
envelope_rg	36.74 Å
shape_rg	36.79 Å
total_rg	36.96 Å
total_atoms	7305
n_residues	928
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	126.8 Å
rg_real	37.01 Å
rg_real_error	1.22 Å
i0_real	3.1910e+08
i0_real_error	5.5910e+06
rg_reciprocal	36.71 Å
i0_reciprocal	319000000.0000
total_estimate	0.7654
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	32.4 Å
skewness	0.621
kurtosis	-0.301
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	53040000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.597; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.545; Smooth: 0.610

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Protein arginine N-methyltransferase 5, N-terminally processed
formula_weight	72766.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7372

MAAMAVGGAGGSRVSSGRDLNCVPEIADTLGAVAKQGFDFLCMPVFHPRFKREFIQEPAKNRPGPQTRSDLLLSGRDWNTLIVGKLSPWIRPDSKVEKIRRNSEAAMLQELNFGAYLGLPAFLLPLNQEDNTNLARVLTNHIHTGHHSSMFWMRVPLVAPEDLRDDIIENAPTTHTEEYSGEEKTWMWWHNFRTLCDYSKRIAVALEIGADLPSNHVIDRWLGEPIKAAILPTSIFLTNKKGFPVLSKMHQRLIFRLLKLEVQFIITGTNHHSEKEFCSYLQYLEYLSQNRPPPNAYELFAKGYEDYLQSPLQPLMDNLESQTYEVFEKDPIKYSQYQQAIYKCLLDRVPEEEKDTNVQVLMVLGAGRGPLVNASLRAAKQADRRIKLYAVEKNPNAVVTLENWQFEEWGSQVTVVSSDMREWVAPEKADIIVSELLGSFADNELSPECLDGAQHFLKDDGVSIPGEYTSFLAPISSSKLYNEVRACREKDRDPEAQFEMPYVVRLHNFHQLSAPQPCFTFSHPNRDPMIDNNRYCTLEFPVEVNTVLHGFAGYFETVLYQDITLSIRPETHSPGMFSWFPILFPIKQPITVREGQTICVRFWRCSNSKKVWYEWAVTAPVCSAIHNPTGRSYTIGL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Methylosome protein WDR77
formula_weight	36757.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MRKETPPPLVPPAAREWNLPPNAPACMERQLEAARYRSDGALLLGASSLSGRCWAGSLWLFKDPCAAPNEGFCSAGVQTEAGVADLTWVGERGILVASDSGAVELWELDENETLIVSKFCKYEHDDIVSTVSVLSSGTQAVSGSKDICIKVWDLAQQVVLSSYRAHAAQVTCVAASPHKDSVFLSCSEDNRILLWDTRCPKPASQIGCSAPGYLPTSLAWHPQQSEVFVFGDENGTVSLVDTKSTSCVLSSAVHSQCVTGLVFSPHSVPFLASLSEDCSLAVLDSSLSELFRSQAHRDFVRDATWSPLNHSLLTTVGWDHQVVHHVVPTEPLPAPGPASVTE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 3 non-polymer

description	;(3~{S})-2-[(5-azanyl-6-fluoranyl-1~{H}-pyrrolo[3,2-b]pyridin-2-yl)methyl]-1'-but-2-ynyl-6-fluoranyl-spiro[isoindole-3,3'-pyrrolidine]-1,2'-dione ;
formula_weight	435.4 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 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	59

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6. Citations (1)

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length_a	102.290 Å
length_b	139.369 Å
length_c	178.549 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	—

resolution	2.180 Å
resolution_low	109.860 Å
r_factor	0.2358
r_work	0.2341
r_free	0.2684

fit	/app/data/saxs_computation/t4/9t43/9t43.fit
pddf	/app/data/pr_computation/t4/9t43/9t43.pr.out
profile	/app/data/saxs_computation/t4/9t43/9t43.dat

Human PRMT5:MEP50 in complex with AZD3470

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)