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9zj1

Crystal structure of SARS-CoV-2 3CL protease in complex with inhibitor NN-IV-169

Method: X-RAY DIFFRACTION D_max: 82.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zj1
deposition_date	2025-12-04
last_revision	2026-06-10
title	Crystal structure of SARS-CoV-2 3CL protease in complex with inhibitor NN-IV-169
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	26.41 Å
rg_electron	25.56 Å
i0	138611000.00
molecular_weight	61874.0 kDa
excluded_volume	59692 Å³
envelope_volume	98480 Å³
shell_volume	31932 Å³
envelope_diameter	85.7 Å
shell_rg	32.97 Å
envelope_rg	25.55 Å
shape_rg	25.54 Å
total_rg	26.16 Å
total_atoms	4650
n_residues	601
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	82.5 Å
rg_real	26.26 Å
rg_real_error	0.35 Å
i0_real	1.3860e+08
i0_real_error	1.7640e+06
rg_reciprocal	26.31 Å
i0_reciprocal	138600000.0000
total_estimate	0.9065
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	35.8 Å
skewness	0.111
kurtosis	-0.599
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	49850000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.981

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	5200

SNIGSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTF

Source

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

Entity 2 non-polymer

description	;N~2~-[({(2R,4S)-3-benzyl-2-oxo-2-[(propan-2-yl)oxy]-1,3,2lambda~5~-oxazaphospholidin-4-yl}methoxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide ;
formula_weight	582.6 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	BROMIDE ION
formula_weight	79.9 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	413

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6. Citations (1)

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length_a	55.431 Å
length_b	98.708 Å
length_c	59.077 Å
angle_alpha	90.00 °
angle_beta	108.15 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.500 Å
resolution_low	46.470 Å
r_factor	0.1685
r_work	0.1673
r_free	0.1915

fit	/app/data/saxs_computation/zj/9zj1/9zj1.fit
pddf	/app/data/pr_computation/zj/9zj1/9zj1.pr.out
profile	/app/data/saxs_computation/zj/9zj1/9zj1.dat

Crystal structure of SARS-CoV-2 3CL protease in complex with inhibitor NN-IV-169

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