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9ri0

SARS-CoV-2 3CL protease with a bound inhibitor

Method: X-RAY DIFFRACTION D_max: 83.7 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ri0
deposition_date	2025-06-10
last_revision	2025-07-09
title	SARS-CoV-2 3CL protease 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	26.59 Å
rg_electron	25.58 Å
i0	77998600.00
molecular_weight	68473.0 kDa
excluded_volume	85332 Å³
envelope_volume	101030 Å³
shell_volume	32560 Å³
envelope_diameter	88.0 Å
shell_rg	33.24 Å
envelope_rg	25.75 Å
shape_rg	25.63 Å
total_rg	26.21 Å
total_atoms	9469
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	83.7 Å
rg_real	26.46 Å
rg_real_error	0.48 Å
i0_real	7.8000e+07
i0_real_error	1.1310e+06
rg_reciprocal	26.51 Å
i0_reciprocal	78000000.0000
total_estimate	0.9051
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	34.9 Å
skewness	0.160
kurtosis	-0.535
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	44710000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.990

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

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	B,A
atom_count	10158

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ

Source

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

Entity 2 non-polymer

description	[1-[[5-chloranyl-1-(phenylmethyl)benzimidazol-2-yl]methyl]-1,2,4-triazol-3-yl]methanamine
formula_weight	352.8 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	604

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6. Citations (1)

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length_a	67.860 Å
length_b	101.850 Å
length_c	104.250 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	1.390 Å
resolution_low	72.853 Å
r_factor	—
r_work	0.1763
r_free	0.1980

fit	/app/data/saxs_computation/ri/9ri0/9ri0.fit
pddf	/app/data/pr_computation/ri/9ri0/9ri0.pr.out
profile	/app/data/saxs_computation/ri/9ri0/9ri0.dat