← Back to search

9znl

X-ray structure of SARS-CoV-2 main protease covalently bound to inhibitor GRL-050-22 at 1.16 A

Method: X-RAY DIFFRACTION D_max: 78.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9znl
deposition_date	2025-12-13
title	X-ray structure of SARS-CoV-2 main protease covalently bound to inhibitor GRL-050-22 at 1.16 A
keywords	;Main protease, 3-chymotrypsin-like protease, Mpro, 3CLpro, Structural Genomics, Center for Structural Biology of Infectious Diseases, CSBID, VIRAL PROTEIN, HYDROLASE, HYDROLASE-INHIBITOR complex ;; VIRAL PROTEIN, HYDROLASE/INHIBITOR
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	22.59 Å
rg_electron	21.81 Å
i0	20928300.00
molecular_weight	34313.0 kDa
excluded_volume	42621 Å³
envelope_volume	50079 Å³
shell_volume	20050 Å³
envelope_diameter	79.8 Å
shell_rg	27.61 Å
envelope_rg	22.00 Å
shape_rg	21.86 Å
total_rg	22.39 Å
total_atoms	4695
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

▼

3. P(r) Analysis (GNOM)

dmax	78.7 Å
rg_real	22.68 Å
rg_real_error	0.63 Å
i0_real	2.0930e+07
i0_real_error	2.8090e+05
rg_reciprocal	22.66 Å
i0_reciprocal	20930000.0000
total_estimate	0.8480
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.7 Å
skewness	0.471
kurtosis	-0.321
angular_range	— – 0.3500 Å⁻¹
current_alpha	0.0000
highest_alpha	8220000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.727; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.887; Smooth: 0.953

▶

4. Crystallography & Experiment

▶

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	5653

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-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-1-(4-phenyl-1,3-thiazol-2-yl)propan-2-yl]-2-[3-methyl-N-(trifluoroacetyl)-L-valyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxamide ;
formula_weight	685.8 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	492

▶

6. Citations (2)

▶

length_a	97.950 Å
length_b	82.339 Å
length_c	54.291 Å
angle_alpha	90.00 °
angle_beta	117.44 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	1.160 Å
resolution_low	20.290 Å
r_factor	0.1414
r_work	0.1411
r_free	0.1594

fit	/app/data/saxs_computation/zn/9znl/9znl.fit
pddf	/app/data/pr_computation/zn/9znl/9znl.pr.out
profile	/app/data/saxs_computation/zn/9znl/9znl.dat

X-ray structure of SARS-CoV-2 main protease covalently bound to inhibitor GRL-050-22 at 1.16 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