SAXSdb — 9zl3

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1. Structure Basics

entry_id	9zl3
deposition_date	2025-12-08
title	Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 18
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	36.38 Å
rg_electron	36.60 Å
i0	342462000.00
molecular_weight	99766.0 kDa
excluded_volume	96285 Å³
envelope_volume	164710 Å³
shell_volume	40500 Å³
envelope_diameter	131.6 Å
shell_rg	39.43 Å
envelope_rg	36.53 Å
shape_rg	36.58 Å
total_rg	36.76 Å
total_atoms	7538
n_residues	920
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	36.84 Å
rg_real_error	1.25 Å
i0_real	3.4250e+08
i0_real_error	6.2520e+06
rg_reciprocal	36.56 Å
i0_reciprocal	342400000.0000
total_estimate	0.7749
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.6 Å
skewness	0.610
kurtosis	-0.305
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	56080000.0000
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: 0.633; Smooth: 0.476

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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	8122

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~2~-(4-amino-1H-pyrazolo[4,3-c]pyridin-7-yl)-N~1~-{(1R)-1-[2-fluoro-4-(trifluoromethyl)phenyl]ethyl}-N~1~-methylethanediamide
formula_weight	424.4 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	8

Entity 6 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	34

Entity 7 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	4

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	487

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6. Citations (1)

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length_a	102.367 Å
length_b	138.128 Å
length_c	178.320 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	1.710 Å
resolution_low	33.620 Å
r_factor	0.1914
r_work	0.1889
r_free	0.2390

fit	/app/data/saxs_computation/zl/9zl3/9zl3.fit
pddf	/app/data/pr_computation/zl/9zl3/9zl3.pr.out
profile	/app/data/saxs_computation/zl/9zl3/9zl3.dat

Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 18

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)