← Back to search

9qrd

SARS-CoV-2 nsp14 with ethyl 2-(1H-indol-3-yl)acetate

Method: X-RAY DIFFRACTION D_max: 87.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9qrd
deposition_date	2025-04-03
last_revision	2026-04-29
title	SARS-CoV-2 nsp14 with ethyl 2-(1H-indol-3-yl)acetate
keywords	SARS-CoV-2, nsp14, Fragment screening, VIRAL PROTEIN; VIRAL PROTEIN
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	26.83 Å
rg_electron	26.45 Å
i0	77379400.00
molecular_weight	46482.0 kDa
excluded_volume	45137 Å³
envelope_volume	76254 Å³
shell_volume	25070 Å³
envelope_diameter	89.0 Å
shell_rg	32.60 Å
envelope_rg	26.64 Å
shape_rg	26.43 Å
total_rg	26.99 Å
total_atoms	3490
n_residues	442
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

▼

3. P(r) Analysis (GNOM)

dmax	87.8 Å
rg_real	26.97 Å
rg_real_error	0.90 Å
i0_real	7.7380e+07
i0_real_error	1.2810e+06
rg_reciprocal	26.93 Å
i0_reciprocal	77380000.0000
total_estimate	0.7927
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	86.3 Å
skewness	0.420
kurtosis	-0.556
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	7158000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.827; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.823; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

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	3841

TMLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQ

Source

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

Entity 2 non-polymer

description	ethyl 2-(1~{H}-indol-3-yl)ethanoate
formula_weight	203.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	3

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	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	326

▶

6. Citations (1)

▶

length_a	67.489 Å
length_b	68.031 Å
length_c	138.117 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	1.910 Å
resolution_low	48.460 Å
r_factor	0.1929
r_work	0.1910
r_free	0.2276

fit	/app/data/saxs_computation/qr/9qrd/9qrd.fit
pddf	/app/data/pr_computation/qr/9qrd/9qrd.pr.out
profile	/app/data/saxs_computation/qr/9qrd/9qrd.dat