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9uoq

Crystal structure of SARS-CoV-2 3CL protease (3CLpro) in complex with compound 8

Method: X-RAY DIFFRACTION D_max: 79.4 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uoq
deposition_date	2025-04-26
title	Crystal structure of SARS-CoV-2 3CL protease (3CLpro) in complex with compound 8
keywords	Mpro, VIRAL PROTEIN-inhibitor complex, 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	22.22 Å
rg_electron	21.66 Å
i0	37305200.00
molecular_weight	31419.0 kDa
excluded_volume	30278 Å³
envelope_volume	49062 Å³
shell_volume	19808 Å³
envelope_diameter	79.3 Å
shell_rg	27.37 Å
envelope_rg	21.87 Å
shape_rg	21.66 Å
total_rg	22.20 Å
total_atoms	2364
n_residues	305
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	79.4 Å
rg_real	22.36 Å
rg_real_error	0.58 Å
i0_real	3.7310e+07
i0_real_error	4.7320e+05
rg_reciprocal	22.33 Å
i0_reciprocal	37300000.0000
total_estimate	0.6250
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	22.5 Å
skewness	0.486
kurtosis	-0.334
angular_range	— – 0.3600 Å⁻¹
current_alpha	0.0000
highest_alpha	11970000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.666; Stabil: 1.000; Sysdev: 0.145; Positv: 1.000; Valcen: 0.698; Smooth: 0.988

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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	2528

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	;(2~{S})-2-[[(2~{S})-3,3-dimethyl-2-[2,2,2-tris(fluoranyl)ethanoylamino]butanoyl]amino]-4-methyl-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]pentanamide ;
formula_weight	478.5 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	131

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6. Citations (1)

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length_a	45.706 Å
length_b	63.581 Å
length_c	105.643 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	1.890 Å
resolution_low	105.640 Å
r_factor	0.2175
r_work	0.2154
r_free	0.2576

fit	/app/data/saxs_computation/uo/9uoq/9uoq.fit
pddf	/app/data/pr_computation/uo/9uoq/9uoq.pr.out
profile	/app/data/saxs_computation/uo/9uoq/9uoq.dat

Crystal structure of SARS-CoV-2 3CL protease (3CLpro) in complex with compound 8

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