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9zj5

Crystal structure of SARS-CoV-2 3CL protease in complex with inhibitor IKR-I-52

Method: X-RAY DIFFRACTION D_max: 75.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zj5
deposition_date	2025-12-04
last_revision	2026-06-10
title	Crystal structure of SARS-CoV-2 3CL protease in complex with inhibitor IKR-I-52
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	22.29 Å
rg_electron	21.72 Å
i0	36961900.00
molecular_weight	31275.0 kDa
excluded_volume	30122 Å³
envelope_volume	49198 Å³
shell_volume	19747 Å³
envelope_diameter	78.3 Å
shell_rg	27.53 Å
envelope_rg	22.03 Å
shape_rg	21.72 Å
total_rg	22.26 Å
total_atoms	2354
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	75.8 Å
rg_real	22.39 Å
rg_real_error	0.57 Å
i0_real	3.6960e+07
i0_real_error	5.1120e+05
rg_reciprocal	22.36 Å
i0_reciprocal	36960000.0000
total_estimate	0.8552
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	21.8 Å
skewness	0.473
kurtosis	-0.371
angular_range	— – 0.3550 Å⁻¹
current_alpha	0.0000
highest_alpha	11650000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.758; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.891; Smooth: 0.951

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	3C-like proteinase
formula_weight	34068.8 kDa
ec_number	3.4.22.69
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2497

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)-3-benzyl-4-methyl-2-oxo-1,3,2lambda~5~-oxazaphospholidin-2-yl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide ;
formula_weight	480.5 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	121

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6. Citations (1)

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length_a	107.488 Å
length_b	52.152 Å
length_c	46.561 Å
angle_alpha	90.00 °
angle_beta	101.43 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.760 Å
resolution_low	46.740 Å
r_factor	0.1703
r_work	0.1676
r_free	0.2179

fit	/app/data/saxs_computation/zj/9zj5/9zj5.fit
pddf	/app/data/pr_computation/zj/9zj5/9zj5.pr.out
profile	/app/data/saxs_computation/zj/9zj5/9zj5.dat

Crystal structure of SARS-CoV-2 3CL protease in complex with inhibitor IKR-I-52

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