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9vs1

Crystal structure of SARS-CoV-2 3CL protease in complex with compound 15

Method: X-RAY DIFFRACTION D_max: 83.6 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vs1
deposition_date	2025-07-08
last_revision	2025-09-24
title	Crystal structure of SARS-CoV-2 3CL protease in complex with compound 15
keywords	VIRAL PROTEIN; VIRAL PROTEIN
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	26.55 Å
rg_electron	25.70 Å
i0	143157000.00
molecular_weight	62755.0 kDa
excluded_volume	60407 Å³
envelope_volume	99898 Å³
shell_volume	32177 Å³
envelope_diameter	88.2 Å
shell_rg	33.26 Å
envelope_rg	25.77 Å
shape_rg	25.69 Å
total_rg	26.28 Å
total_atoms	4719
n_residues	603
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	83.6 Å
rg_real	26.41 Å
rg_real_error	0.52 Å
i0_real	1.4320e+08
i0_real_error	2.0570e+06
rg_reciprocal	26.46 Å
i0_reciprocal	143200000.0000
total_estimate	0.9063
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	36.2 Å
skewness	0.123
kurtosis	-0.584
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	46370000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.998

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	3C-like proteinase
formula_weight	33969.7 kDa
ec_number	3.4.22.69
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5224

GSSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ

Source

organism	Severe acute respiratory syndrome coronavirus 2
common_name	2019-nCoV,SARS-CoV-2
ncbi_taxonomy_id	2697049
host_organism	Escherichia coli

Entity 2 non-polymer

description	;4-chloranyl-3-[6-methyl-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-2,4,5-tris(oxidanylidene)-1-[[3,4,5-tris(fluoranyl)phenyl]methyl]pyrido[4,3-d]pyrimidin-7-yl]benzenecarbonitrile ;
formula_weight	567.9 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

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

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	448

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6. Citations (1)

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length_a	55.801 Å
length_b	98.639 Å
length_c	59.655 Å
angle_alpha	90.00 °
angle_beta	108.42 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.700 Å
resolution_low	56.600 Å
r_factor	0.1780
r_work	0.1757
r_free	0.2232

fit	/app/data/saxs_computation/vs/9vs1/9vs1.fit
pddf	/app/data/pr_computation/vs/9vs1/9vs1.pr.out
profile	/app/data/saxs_computation/vs/9vs1/9vs1.dat

Crystal structure of SARS-CoV-2 3CL protease in complex with compound 15

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