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9zj6

Crystal structure of SARS-CoV-2 3CL protease in complex with inhibitor PSR-I-162

Method: X-RAY DIFFRACTION D_max: 83.2 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zj6
deposition_date	2025-12-04
last_revision	2026-06-10
title	Crystal structure of SARS-CoV-2 3CL protease in complex with inhibitor PSR-I-162
keywords	HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/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	26.53 Å
rg_electron	25.67 Å
i0	143247000.00
molecular_weight	62789.0 kDa
excluded_volume	60478 Å³
envelope_volume	99857 Å³
shell_volume	32211 Å³
envelope_diameter	87.4 Å
shell_rg	33.15 Å
envelope_rg	25.78 Å
shape_rg	25.66 Å
total_rg	26.25 Å
total_atoms	4722
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	83.2 Å
rg_real	26.39 Å
rg_real_error	0.54 Å
i0_real	1.4320e+08
i0_real_error	2.1180e+06
rg_reciprocal	26.43 Å
i0_reciprocal	143300000.0000
total_estimate	0.9064
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	36.0 Å
skewness	0.132
kurtosis	-0.571
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	47480000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.930; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.990

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	3C-like proteinase
formula_weight	34068.8 kDa
ec_number	3.4.22.69
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5181

SNIGSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTF

Source

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

Entity 2 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	;methyl (2R,4S)-3-benzyl-2-{[(2S)-1-{[(1S,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-1-(trihydroxy-lambda~4~-sulfanyl)propan-2-yl]amino}-4-methyl-1-oxopentan-2-yl]amino}-2-oxo-1,3,2lambda~5~-oxazaphospholidine-4-carboxylate ;
formula_weight	604.6 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	406

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6. Citations (1)

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length_a	55.525 Å
length_b	98.920 Å
length_c	58.903 Å
angle_alpha	90.00 °
angle_beta	108.26 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.520 Å
resolution_low	49.460 Å
r_factor	0.1618
r_work	0.1608
r_free	0.1810

fit	/app/data/saxs_computation/zj/9zj6/9zj6.fit
pddf	/app/data/pr_computation/zj/9zj6/9zj6.pr.out
profile	/app/data/saxs_computation/zj/9zj6/9zj6.dat