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9riy

SARS-CoV-2 with a bound inhibitor

Method: X-RAY DIFFRACTION D_max: 82.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9riy
deposition_date	2025-06-12
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	26.51 Å
rg_electron	25.47 Å
i0	76295600.00
molecular_weight	67585.0 kDa
excluded_volume	84122 Å³
envelope_volume	99384 Å³
shell_volume	32256 Å³
envelope_diameter	87.0 Å
shell_rg	33.05 Å
envelope_rg	25.58 Å
shape_rg	25.52 Å
total_rg	26.11 Å
total_atoms	9330
n_residues	605
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	82.8 Å
rg_real	26.38 Å
rg_real_error	0.54 Å
i0_real	7.6300e+07
i0_real_error	1.1480e+06
rg_reciprocal	26.42 Å
i0_reciprocal	76300000.0000
total_estimate	0.9074
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	80.1 Å
skewness	0.151
kurtosis	-0.550
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	37340000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.934; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.991

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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	9551

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ

Source

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

Entity 2 non-polymer

description	[6-(4-iodanylphenoxy)pyrimidin-4-yl]methanimine
formula_weight	325.1 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	221

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6. Citations (1)

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length_a	67.760 Å
length_b	99.540 Å
length_c	103.520 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	1.788 Å
resolution_low	71.751 Å
r_factor	—
r_work	0.2142
r_free	0.2577

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