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9vao

Crystal structure of Papain-like protease (PLpro) from SARS-CoV-2

Method: X-RAY DIFFRACTION D_max: 92.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vao
deposition_date	2025-06-03
title	Crystal structure of Papain-like protease (PLpro) from SARS-CoV-2
keywords	Cysteine Protease, PLpro, SARS-CoV-2, Ubl domain, VIRAL PROTEIN; VIRAL PROTEIN
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	24.34 Å
rg_electron	23.71 Å
i0	23458800.00
molecular_weight	36559.0 kDa
excluded_volume	45517 Å³
envelope_volume	55181 Å³
shell_volume	21059 Å³
envelope_diameter	99.1 Å
shell_rg	28.77 Å
envelope_rg	24.39 Å
shape_rg	23.60 Å
total_rg	24.67 Å
total_atoms	2557
n_residues	317
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	92.0 Å
rg_real	24.63 Å
rg_real_error	0.95 Å
i0_real	2.3460e+07
i0_real_error	3.8040e+05
rg_reciprocal	24.56 Å
i0_reciprocal	23460000.0000
total_estimate	0.7780
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.8 Å
skewness	0.653
kurtosis	0.157
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	4122000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.570; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.489; Smooth: 0.910

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Papain-like protease nsp3
formula_weight	35898.7 kDa
ec_number	3.4.19.12,3.4.22.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2920

SHMEVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTI

Source

organism	Severe acute respiratory syndrome coronavirus 2
common_name	2019-nCoV, SARS-CoV-2
ncbi_taxonomy_id	2697049
host_organism	Escherichia coli

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	5

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	313

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6. Citations (1)

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length_a	81.821 Å
length_b	81.821 Å
length_c	133.733 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 32 2 1
int_tables_number	154
crystal_system	trigonal

resolution	1.820 Å
resolution_low	48.630 Å
r_factor	0.1901
r_work	0.1886
r_free	0.2239

fit	/app/data/saxs_computation/va/9vao/9vao.fit
pddf	/app/data/pr_computation/va/9vao/9vao.pr.out
profile	/app/data/saxs_computation/va/9vao/9vao.dat