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9sdm

;Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the covalently bound inhibitor GUE-4303 (compound 12 in publication) ;

Method: X-RAY DIFFRACTION D_max: 83.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sdm
deposition_date	2025-08-14
last_revision	2026-01-14
title	;Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the covalently bound inhibitor GUE-4303 (compound 12 in publication) ;
keywords	main protease, ANTIVIRAL PROTEIN; ANTIVIRAL 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	26.60 Å
rg_electron	25.55 Å
i0	77768900.00
molecular_weight	68416.0 kDa
excluded_volume	85236 Å³
envelope_volume	100810 Å³
shell_volume	32551 Å³
envelope_diameter	87.6 Å
shell_rg	33.16 Å
envelope_rg	25.65 Å
shape_rg	25.60 Å
total_rg	26.18 Å
total_atoms	9428
n_residues	606
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	83.4 Å
rg_real	26.47 Å
rg_real_error	0.52 Å
i0_real	7.7770e+07
i0_real_error	1.1590e+06
rg_reciprocal	26.51 Å
i0_reciprocal	77770000.0000
total_estimate	0.9068
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	34.7 Å
skewness	0.156
kurtosis	-0.540
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	39530000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.995

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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	9958

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ

Source

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

Entity 2 non-polymer

description	;N-[(2S)-1-[[(2S)-1-[2-[(3-chlorophenyl)methyl]-2-ethanoyl-hydrazinyl]-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-3,3-dimethyl-1-oxidanylidene-butan-2-yl]thiophene-2-carboxamide ;
formula_weight	569.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	CARBONATE ION
formula_weight	60.0 kDa
src_method	nat
entity_count	3

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	472

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6. Citations (1)

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length_a	67.838 Å
length_b	101.727 Å
length_c	104.045 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	1.550 Å
resolution_low	36.370 Å
r_factor	0.1895
r_work	0.1874
r_free	0.2311

fit	/app/data/saxs_computation/sd/9sdm/9sdm.fit
pddf	/app/data/pr_computation/sd/9sdm/9sdm.pr.out
profile	/app/data/saxs_computation/sd/9sdm/9sdm.dat