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9z74

X-ray structure of SARS-CoV-2 main protease V186G covalently bound to inhibitor Nirmatrelvir at 1.81 A

Method: X-RAY DIFFRACTION D_max: 75.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z74
deposition_date	2025-11-16
title	X-ray structure of SARS-CoV-2 main protease V186G covalently bound to inhibitor Nirmatrelvir at 1.81 A
keywords	;Main protease, 3-chymotrypsin-like protease, Mpro, 3CLpro, Mutant, Structural Genomics, Center for Structural Biology of Infectious Diseases, CSBID, VIRAL PROTEIN, HYDROLASE, HYDROLASE-INHIBITOR complex ;; 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	22.44 Å
rg_electron	21.72 Å
i0	20753300.00
molecular_weight	34252.0 kDa
excluded_volume	42665 Å³
envelope_volume	49663 Å³
shell_volume	19987 Å³
envelope_diameter	76.6 Å
shell_rg	27.61 Å
envelope_rg	21.90 Å
shape_rg	21.71 Å
total_rg	22.53 Å
total_atoms	4740
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	75.5 Å
rg_real	22.54 Å
rg_real_error	0.64 Å
i0_real	2.0750e+07
i0_real_error	2.9740e+05
rg_reciprocal	22.51 Å
i0_reciprocal	20750000.0000
total_estimate	0.8630
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.9 Å
skewness	0.477
kurtosis	-0.331
angular_range	— – 0.3550 Å⁻¹
current_alpha	0.0000
highest_alpha	8416000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.773; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.923; Smooth: 0.979

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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	33783.5 kDa
ec_number	3.4.22.69
mutation	V186G
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5255

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFGDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ

Source

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

Entity 2 non-polymer

description	;(1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide ;
formula_weight	501.5 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	355

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6. Citations (2)

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length_a	45.660 Å
length_b	63.534 Å
length_c	105.442 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	1.810 Å
resolution_low	54.420 Å
r_factor	0.1657
r_work	0.1637
r_free	0.2058

fit	/app/data/saxs_computation/z7/9z74/9z74.fit
pddf	/app/data/pr_computation/z7/9z74/9z74.pr.out
profile	/app/data/saxs_computation/z7/9z74/9z74.dat

X-ray structure of SARS-CoV-2 main protease V186G covalently bound to inhibitor Nirmatrelvir at 1.81 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