SAXSdb — 9qca

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1. Structure Basics

entry_id	9qca
deposition_date	2025-03-04
last_revision	2026-03-18
title	PRMT2 in complex with MMA analog
keywords	protein arginine N-methyltransferase, PRMT, PRMT2, transition state analogs, transcription, 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	22.99 Å
rg_electron	22.13 Å
i0	26032500.00
molecular_weight	40027.0 kDa
excluded_volume	50422 Å³
envelope_volume	58625 Å³
shell_volume	22721 Å³
envelope_diameter	80.3 Å
shell_rg	28.36 Å
envelope_rg	22.59 Å
shape_rg	22.10 Å
total_rg	23.00 Å
total_atoms	5582
n_residues	343
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	79.9 Å
rg_real	23.03 Å
rg_real_error	0.66 Å
i0_real	2.6030e+07
i0_real_error	3.9070e+05
rg_reciprocal	23.02 Å
i0_reciprocal	26030000.0000
total_estimate	0.7852
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.8 Å
skewness	0.450
kurtosis	-0.182
angular_range	— – 0.3450 Å⁻¹
current_alpha	0.0000
highest_alpha	5534000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.751; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.950; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Protein arginine N-methyltransferase 2
formula_weight	50745.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6032

GHMEAPGEGPCSESQVIPVLEEDPVDYGCEMQLLQDGAQLQLQLQPEEFVAIADYTATDETQLSFLRGEKILILRQTTADWWWGERAGCCGYIPANHLGKQLEEYDPEDTWQDEEYFDSYGTLKLHLEMLADQPRTTKYHSVILQNKESLKDKVILDVGCGTGIISLFCAHHARPKAVYAVEASDMAQHTSQLVLQNGFADTITVFQQKVEDVVLPEKVDVLVSEWMGTCLLFEFMIESILYARDTWLKGDGIIWPTTAALHLVPCSAEKDYHSKVLFWDNAYEFNLSALKSLAIKEFFSRPKSNHILKPEDCLSEPCTILQLDMRTVQVPDLETMRGELRFDIQKAGTLHGFTAWFSVYFQSLEEGQPQQVLSTGPLHPTTHWKQTLFMMDDPVPVHTGDVVTGSVVLQRNPVWRRHMSVSLSWVVTSALDPTSQRVGEKVFPIWR

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Spodoptera aff. frugiperda 1 BOLD-2017

Entity 2 non-polymer

description	;(phenylmethyl) (2S)-5-[[N-[3-[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]propyl]carbamimidoyl]amino]-2-(phenylmethoxycarbonylamino)pentanoate ;
formula_weight	675.7 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
formula_weight	238.3 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	450

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6. Citations (1)

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length_a	66.405 Å
length_b	114.994 Å
length_c	133.226 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	1.730 Å
resolution_low	29.720 Å
r_factor	0.1658
r_work	0.1648
r_free	0.1854

fit	/app/data/saxs_computation/qc/9qca/9qca.fit
pddf	/app/data/pr_computation/qc/9qca/9qca.pr.out
profile	/app/data/saxs_computation/qc/9qca/9qca.dat

PRMT2 in complex with MMA analog

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