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9zo3

X-ray structure of SARS-CoV-2 main protease covalently bound to inhibitor GRL-062-22 at 1.65 A

Method: X-RAY DIFFRACTION D_max: 77.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zo3
deposition_date	2025-12-15
title	X-ray structure of SARS-CoV-2 main protease covalently bound to inhibitor GRL-062-22 at 1.65 A
keywords	;SARS-CoV-2, Main protease, 3CLpro, CSBID, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex, Structural Genomics, Center for Structural Biology of Infectious Diseases ;; VIRAL PROTEIN, HYDROLASE/INHIBITOR
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	22.57 Å
rg_electron	21.84 Å
i0	20814500.00
molecular_weight	34435.0 kDa
excluded_volume	42874 Å³
envelope_volume	50116 Å³
shell_volume	20050 Å³
envelope_diameter	78.5 Å
shell_rg	27.74 Å
envelope_rg	22.05 Å
shape_rg	21.92 Å
total_rg	22.38 Å
total_atoms	4729
n_residues	306
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	77.4 Å
rg_real	22.67 Å
rg_real_error	0.59 Å
i0_real	2.0810e+07
i0_real_error	3.0240e+05
rg_reciprocal	22.65 Å
i0_reciprocal	20810000.0000
total_estimate	0.8583
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.3 Å
skewness	0.481
kurtosis	-0.313
angular_range	— – 0.3500 Å⁻¹
current_alpha	0.0000
highest_alpha	8077000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.752; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.905; Smooth: 0.993

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	5289

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ

Source

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

Entity 2 non-polymer

description	;(3S)-N-{(1S,2S)-1-(1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopiperidin-3-yl]propan-2-yl}-2-[3-methyl-N-(trifluoroacetyl)-L-valyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxamide ;
formula_weight	673.7 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	385

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6. Citations (2)

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length_a	45.958 Å
length_b	63.229 Å
length_c	105.517 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	orthorhombic

resolution	1.650 Å
resolution_low	30.740 Å
r_factor	0.1609
r_work	0.1590
r_free	0.1956

fit	/app/data/saxs_computation/zo/9zo3/9zo3.fit
pddf	/app/data/pr_computation/zo/9zo3/9zo3.pr.out
profile	/app/data/saxs_computation/zo/9zo3/9zo3.dat

X-ray structure of SARS-CoV-2 main protease covalently bound to inhibitor GRL-062-22 at 1.65 A

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