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9rj5

SARS-CoV-2 with a bound inhibitor

Method: X-RAY DIFFRACTION D_max: 79.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rj5
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	22.55 Å
rg_electron	21.82 Å
i0	18931200.00
molecular_weight	32977.0 kDa
excluded_volume	41244 Å³
envelope_volume	48468 Å³
shell_volume	19535 Å³
envelope_diameter	79.4 Å
shell_rg	27.50 Å
envelope_rg	22.02 Å
shape_rg	21.88 Å
total_rg	22.37 Å
total_atoms	4588
n_residues	297
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	79.3 Å
rg_real	22.68 Å
rg_real_error	0.58 Å
i0_real	1.8930e+07
i0_real_error	2.6290e+05
rg_reciprocal	22.65 Å
i0_reciprocal	18930000.0000
total_estimate	0.8359
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.8 Å
skewness	0.510
kurtosis	-0.302
angular_range	— – 0.3500 Å⁻¹
current_alpha	0.0000
highest_alpha	8677000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.674; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.844; Smooth: 0.996

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	3C-like proteinase nsp5
formula_weight	33825.5 kDa
ec_number	3.4.22.69
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5012

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ

Source

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

Entity 2 non-polymer

description	1-(2-cyclohexylethyl)-3-cyclopropyl-1-[(5-methyl-1,2-oxazol-3-yl)methyl]urea
formula_weight	305.4 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	281

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6. Citations (1)

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length_a	97.800 Å
length_b	81.760 Å
length_c	51.720 Å
angle_alpha	90.00 °
angle_beta	114.67 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.250 Å
resolution_low	47.004 Å
r_factor	—
r_work	0.1509
r_free	0.1764

fit	/app/data/saxs_computation/rj/9rj5/9rj5.fit
pddf	/app/data/pr_computation/rj/9rj5/9rj5.pr.out
profile	/app/data/saxs_computation/rj/9rj5/9rj5.dat

SARS-CoV-2 with a bound inhibitor

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction