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9qxb

SARS-CoV-2 nsp14 with N-methyl-1-(2-methyl-5-phenylpyrazol-3-yl)methanamine

Method: X-RAY DIFFRACTION D_max: 87.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qxb
deposition_date	2025-04-15
last_revision	2026-04-29
title	SARS-CoV-2 nsp14 with N-methyl-1-(2-methyl-5-phenylpyrazol-3-yl)methanamine
keywords	SARS-CoV-2, nsp14, Fragment screening, VIRAL PROTEIN; VIRAL PROTEIN
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	27.02 Å
rg_electron	26.49 Å
i0	43675800.00
molecular_weight	51295.0 kDa
excluded_volume	64028 Å³
envelope_volume	77839 Å³
shell_volume	25582 Å³
envelope_diameter	89.5 Å
shell_rg	32.68 Å
envelope_rg	26.59 Å
shape_rg	26.50 Å
total_rg	27.16 Å
total_atoms	3589
n_residues	451
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	87.2 Å
rg_real	27.15 Å
rg_real_error	0.72 Å
i0_real	4.3680e+07
i0_real_error	6.7550e+05
rg_reciprocal	27.11 Å
i0_reciprocal	43670000.0000
total_estimate	0.8765
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.1 Å
skewness	0.410
kurtosis	-0.528
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	5229000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.868; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.888; Smooth: 0.897

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Guanine-N7 methyltransferase nsp14
formula_weight	59548.2 kDa
ec_number	2.1.1.56,3.1.13.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3822

TMLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQ

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Escherichia coli

Entity 2 non-polymer

description	methyl-3-methyl-5-phenyl-2H-pyrazol-4-methyl amine
formula_weight	201.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	5

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	212

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6. Citations (1)

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length_a	67.090 Å
length_b	67.770 Å
length_c	138.550 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.840 Å
resolution_low	48.440 Å
r_factor	0.2275
r_work	0.2261
r_free	0.2522

fit	/app/data/saxs_computation/qx/9qxb/9qxb.fit
pddf	/app/data/pr_computation/qx/9qxb/9qxb.pr.out
profile	/app/data/saxs_computation/qx/9qxb/9qxb.dat