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9zzh

Crystal structure of SARS-CoV-2 3CL protease in complex with inhibitor CSD-V-169

Method: X-RAY DIFFRACTION D_max: 83.7 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zzh
deposition_date	2026-01-07
last_revision	2026-06-10
title	Crystal structure of SARS-CoV-2 3CL protease in complex with inhibitor CSD-V-169
keywords	;PROTEASE, SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS 2, SARS-COV-2 3CL PROTEASE INHHIBITORS, COVID-19, VIRAL PROTEIN, HYDROLASE-HYDROLASE INHIBITOR COMPLEX, HYDROLASE ;; 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	26.34 Å
rg_electron	25.48 Å
i0	141839000.00
molecular_weight	62467.0 kDa
excluded_volume	60155 Å³
envelope_volume	99028 Å³
shell_volume	32070 Å³
envelope_diameter	88.6 Å
shell_rg	33.05 Å
envelope_rg	25.63 Å
shape_rg	25.47 Å
total_rg	26.07 Å
total_atoms	4696
n_residues	607
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	83.7 Å
rg_real	26.20 Å
rg_real_error	0.53 Å
i0_real	1.4180e+08
i0_real_error	2.0130e+06
rg_reciprocal	26.24 Å
i0_reciprocal	141800000.0000
total_estimate	0.9037
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	34.9 Å
skewness	0.133
kurtosis	-0.570
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	47290000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.995

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

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	4924

SNIGSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTF

Source

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

Entity 2 non-polymer

description	;methyl (2S,4R)-3-benzyl-2-{[(2S)-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]amino}-2-oxo-1,3,2lambda~5~-oxazaphospholidine-4-carboxylate ;
formula_weight	524.5 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	222

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6. Citations (1)

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length_a	54.946 Å
length_b	98.931 Å
length_c	58.507 Å
angle_alpha	90.00 °
angle_beta	107.52 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.870 Å
resolution_low	49.470 Å
r_factor	0.1737
r_work	0.1718
r_free	0.2120

fit	/app/data/saxs_computation/zz/9zzh/9zzh.fit
pddf	/app/data/pr_computation/zz/9zzh/9zzh.pr.out
profile	/app/data/saxs_computation/zz/9zzh/9zzh.dat