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9s2v

NSP14 IN COMPLEX WITH LIGAND TDI-014925-CL-2 (compound 58)

Method: X-RAY DIFFRACTION D_max: 98.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s2v
deposition_date	2025-07-22
title	NSP14 IN COMPLEX WITH LIGAND TDI-014925-CL-2 (compound 58)
keywords	NOVEL CORONAVIRUS, 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	32.14 Å
rg_electron	31.42 Å
i0	316238000.00
molecular_weight	95620.0 kDa
excluded_volume	92600 Å³
envelope_volume	164590 Å³
shell_volume	42771 Å³
envelope_diameter	106.7 Å
shell_rg	39.29 Å
envelope_rg	31.13 Å
shape_rg	31.40 Å
total_rg	31.94 Å
total_atoms	7184
n_residues	878
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	98.5 Å
rg_real	31.96 Å
rg_real_error	0.49 Å
i0_real	3.1620e+08
i0_real_error	4.2580e+06
rg_reciprocal	32.04 Å
i0_reciprocal	316300000.0000
total_estimate	0.9085
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	42.2 Å
skewness	0.103
kurtosis	-0.622
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0001
highest_alpha	29620000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.928

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Guanine-N7 methyltransferase nsp14
formula_weight	59872.5 kDa
ec_number	2.1.1.56,3.1.13.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7391

SAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFAVAGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQ

Source

organism	SARS-CoV-2 pseudovirus
ncbi_taxonomy_id	3092168
host_organism	Escherichia coli

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	6

Entity 3 non-polymer

description	S-ADENOSYL-L-HOMOCYSTEINE
formula_weight	384.4 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	;~{N}-[(6-fluoranyl-1-methyl-indazol-7-yl)methyl]-1,5-dimethyl-4-(1,4,6,7-tetrahydropyrazolo[4,3-c]pyridin-5-ylsulfonyl)pyrrole-2-carboxamide ;
formula_weight	485.5 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	5

Entity 6 non-polymer

description	IMIDAZOLE
formula_weight	69.1 kDa
src_method	syn
entity_count	2

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	207

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6. Citations (1)

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length_a	67.458 Å
length_b	100.962 Å
length_c	90.426 Å
angle_alpha	90.00 °
angle_beta	108.33 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.380 Å
resolution_low	64.120 Å
r_factor	0.1943
r_work	0.1931
r_free	0.2452

fit	/app/data/saxs_computation/s2/9s2v/9s2v.fit
pddf	/app/data/pr_computation/s2/9s2v/9s2v.pr.out
profile	/app/data/saxs_computation/s2/9s2v/9s2v.dat