SAXSdb — 9zl4

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1. Structure Basics

entry_id	9zl4
deposition_date	2025-12-08
title	Crystal structure of PRMT5:MEP50 in complex with MTA and TNG456
keywords	methyltransferase, SAM, MTAP-null, MTA-cooperative, TRANSFERASE, TRANSFERASE-INHIBITOR complex; 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	36.45 Å
rg_electron	36.70 Å
i0	343798000.00
molecular_weight	99928.0 kDa
excluded_volume	96425 Å³
envelope_volume	164620 Å³
shell_volume	40488 Å³
envelope_diameter	132.8 Å
shell_rg	39.32 Å
envelope_rg	36.57 Å
shape_rg	36.69 Å
total_rg	36.84 Å
total_atoms	7551
n_residues	922
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	127.0 Å
rg_real	36.92 Å
rg_real_error	1.21 Å
i0_real	3.4380e+08
i0_real_error	5.8530e+06
rg_reciprocal	36.63 Å
i0_reciprocal	343700000.0000
total_estimate	0.7681
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	32.5 Å
skewness	0.615
kurtosis	-0.308
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	60010000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.593; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.549; Smooth: 0.652

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

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	8388

MDYKDDDDKAAMAVGGAGGSRVSSGRDLNCVPEIADTLGAVAKQGFDFLCMPVFHPRFKREFIQEPAKNRPGPQTRSDLLLSGRDWNTLIVGKLSPWIRPDSKVEKIRRNSEAAMLQELNFGAYLGLPAFLLPLNQEDNTNLARVLTNHIHTGHHSSMFWMRVPLVAPEDLRDDIIENAPTTHTEEYSGEEKTWMWWHNFRTLCDYSKRIAVALEIGADLPSNHVIDRWLGEPIKAAILPTSIFLTNKKGFPVLSKMHQRLIFRLLKLEVQFIITGTNHHSEKEFCSYLQYLEYLSQNRPPPNAYELFAKGYEDYLQSPLQPLMDNLESQTYEVFEKDPIKYSQYQQAIYKCLLDRVPEEEKDTNVQVLMVLGAGRGPLVNASLRAAKQADRRIKLYAVEKNPNAVVTLENWQFEEWGSQVTVVSSDMREWVAPEKADIIVSELLGSFADNELSPECLDGAQHFLKDDGVSIPGEYTSFLAPISSSKLYNEVRACREKDRDPEAQFEMPYVVRLHNFHQLSAPQPCFTFSHPNRDPMIDNNRYCTLEFPVEVNTVLHGFAGYFETVLYQDITLSIRPETHSPGMFSWFPILFPIKQPITVREGQTICVRFWRCSNSKKVWYEWAVTAPVCSAIHNPTGRSYTIGL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

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	Trichoplusia ni

Entity 3 non-polymer

description	N~2~-(4-amino-1H-pyrazolo[4,3-c]pyridin-7-yl)-N~1~-methyl-N~1~-{(1R)-1-[4-(trifluoromethyl)phenyl]ethyl}ethanediamide
formula_weight	406.4 kDa
src_method	syn
entity_count	2

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	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	4

Entity 7 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	39

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	705

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6. Citations (1)

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length_a	100.510 Å
length_b	138.260 Å
length_c	178.290 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	1.950 Å
resolution_low	45.660 Å
r_factor	0.1793
r_work	0.1762
r_free	0.2361

fit	/app/data/saxs_computation/zl/9zl4/9zl4.fit
pddf	/app/data/pr_computation/zl/9zl4/9zl4.pr.out
profile	/app/data/saxs_computation/zl/9zl4/9zl4.dat

Crystal structure of PRMT5:MEP50 in complex with MTA and TNG456

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 (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)