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9ri3

SARS-CoV-2 with a bound inhibitor

Method: X-RAY DIFFRACTION D_max: 83.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ri3
deposition_date	2025-06-11
last_revision	2025-07-09
title	SARS-CoV-2 with a bound inhibitor
keywords	protease, inhibitor, HYDROLASE; HYDROLASE
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	26.63 Å
rg_electron	25.59 Å
i0	77428600.00
molecular_weight	68038.0 kDa
excluded_volume	84748 Å³
envelope_volume	101510 Å³
shell_volume	32698 Å³
envelope_diameter	87.8 Å
shell_rg	33.26 Å
envelope_rg	25.73 Å
shape_rg	25.64 Å
total_rg	26.22 Å
total_atoms	9407
n_residues	610
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	83.8 Å
rg_real	26.50 Å
rg_real_error	0.44 Å
i0_real	7.7430e+07
i0_real_error	9.7230e+05
rg_reciprocal	26.54 Å
i0_reciprocal	77430000.0000
total_estimate	0.9054
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	34.9 Å
skewness	0.152
kurtosis	-0.539
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	40490000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.994

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	3C-like proteinase nsp5
formula_weight	33825.5 kDa
ec_number	3.4.22.69
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	9610

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ

Source

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

Entity 2 non-polymer

description	[1-(2-methylsulfanyl-[1,3]thiazolo[4,5-d]pyrimidin-7-yl)-1,2,4-triazol-3-yl]methanimine
formula_weight	277.3 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	203

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6. Citations (1)

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length_a	67.940 Å
length_b	100.900 Å
length_c	104.840 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.723 Å
resolution_low	72.700 Å
r_factor	—
r_work	0.2104
r_free	0.2383

fit	/app/data/saxs_computation/ri/9ri3/9ri3.fit
pddf	/app/data/pr_computation/ri/9ri3/9ri3.pr.out
profile	/app/data/saxs_computation/ri/9ri3/9ri3.dat