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9zj3

Crystal structure of SARS-CoV-2 3CL protease in complex with inhibitor AMJ-II-72

Method: X-RAY DIFFRACTION D_max: 79.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zj3
deposition_date	2025-12-04
last_revision	2026-06-10
title	Crystal structure of SARS-CoV-2 3CL protease in complex with inhibitor AMJ-II-72
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	26.36 Å
rg_electron	25.52 Å
i0	134115000.00
molecular_weight	60903.0 kDa
excluded_volume	58785 Å³
envelope_volume	96627 Å³
shell_volume	31374 Å³
envelope_diameter	85.8 Å
shell_rg	33.05 Å
envelope_rg	25.52 Å
shape_rg	25.51 Å
total_rg	26.11 Å
total_atoms	4579
n_residues	598
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	79.7 Å
rg_real	26.22 Å
rg_real_error	0.47 Å
i0_real	1.3410e+08
i0_real_error	1.6970e+06
rg_reciprocal	26.26 Å
i0_reciprocal	134100000.0000
total_estimate	0.8364
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.2 Å
skewness	0.108
kurtosis	-0.600
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	47730000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.957; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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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	4764

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~-({[(2S,4R)-2-[(4-fluorophenyl)methoxy]-3-(2-methylpropyl)-2-oxo-1,3,2lambda~5~-oxazaphospholidin-4-yl]methoxy}carbonyl)-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide ;
formula_weight	612.6 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	177

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6. Citations (1)

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length_a	55.328 Å
length_b	98.430 Å
length_c	59.391 Å
angle_alpha	90.00 °
angle_beta	108.34 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.100 Å
resolution_low	46.390 Å
r_factor	0.1739
r_work	0.1711
r_free	0.2308

fit	/app/data/saxs_computation/zj/9zj3/9zj3.fit
pddf	/app/data/pr_computation/zj/9zj3/9zj3.pr.out
profile	/app/data/saxs_computation/zj/9zj3/9zj3.dat

Crystal structure of SARS-CoV-2 3CL protease in complex with inhibitor AMJ-II-72

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