SAXSdb — 9zl2

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1. Structure Basics

entry_id	9zl2
deposition_date	2025-12-08
title	Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 8
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	36.40 Å
rg_electron	36.60 Å
i0	328160000.00
molecular_weight	97736.0 kDa
excluded_volume	94447 Å³
envelope_volume	164830 Å³
shell_volume	40564 Å³
envelope_diameter	131.2 Å
shell_rg	39.34 Å
envelope_rg	36.58 Å
shape_rg	36.58 Å
total_rg	36.78 Å
total_atoms	7402
n_residues	927
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	123.7 Å
rg_real	36.85 Å
rg_real_error	1.20 Å
i0_real	3.2820e+08
i0_real_error	5.5660e+06
rg_reciprocal	36.57 Å
i0_reciprocal	328100000.0000
total_estimate	0.7756
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.6 Å
skewness	0.615
kurtosis	-0.296
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	54310000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.658; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.637; Smooth: 0.467

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

Entity 4 non-polymer

description	N~1~,N~1~-dibenzyl-N~2~-(5-carbamoylpyridin-3-yl)ethanediamide
formula_weight	388.4 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	18

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6. Citations (1)

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length_a	101.420 Å
length_b	136.780 Å
length_c	178.140 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	3.180 Å
resolution_low	45.940 Å
r_factor	0.2617
r_work	0.2600
r_free	0.2934

fit	/app/data/saxs_computation/zl/9zl2/9zl2.fit
pddf	/app/data/pr_computation/zl/9zl2/9zl2.pr.out
profile	/app/data/saxs_computation/zl/9zl2/9zl2.dat

Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 8

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)