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9pvi

SARS-CoV-2 Papain-like Protease (PLpro) in complex with Fragment 47

Method: X-RAY DIFFRACTION D_max: 88.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9pvi
deposition_date	2025-08-01
title	SARS-CoV-2 Papain-like Protease (PLpro) in complex with Fragment 47
keywords	Viral protease, Inhibitor complex, 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	23.24 Å
rg_electron	22.72 Å
i0	37783600.00
molecular_weight	31984.0 kDa
excluded_volume	31038 Å³
envelope_volume	51581 Å³
shell_volume	20383 Å³
envelope_diameter	94.4 Å
shell_rg	27.97 Å
envelope_rg	23.41 Å
shape_rg	22.64 Å
total_rg	23.36 Å
total_atoms	2414
n_residues	305
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	88.8 Å
rg_real	23.45 Å
rg_real_error	0.84 Å
i0_real	3.7780e+07
i0_real_error	5.1890e+05
rg_reciprocal	23.40 Å
i0_reciprocal	37780000.0000
total_estimate	0.7073
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	23.2 Å
skewness	0.622
kurtosis	0.087
angular_range	— – 0.3400 Å⁻¹
current_alpha	0.0000
highest_alpha	7262000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.537; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.579; Smooth: 0.000

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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	37096.0 kDa
ec_number	3.4.19.12,3.4.22.-
mutation	C111S
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2562

MREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNSYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQSGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPLEHHHHHH

Source

organism	Severe acute respiratory syndrome coronavirus 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	;(7M)-8-methyl-7-(2-methylpyridin-4-yl)-1'-{[(6P)-6-(1H-pyrazol-5-yl)pyridin-2-yl]methyl}-3,4-dihydrospiro[[1]benzopyran-2,4'-piperidine] ;
formula_weight	465.6 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	128

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6. Citations (1)

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length_a	79.347 Å
length_b	79.347 Å
length_c	232.837 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 65 2 2
int_tables_number	179
crystal_system	hexagonal

resolution	1.800 Å
resolution_low	33.790 Å
r_factor	0.2254
r_work	0.2237
r_free	0.2574

fit	/app/data/saxs_computation/pv/9pvi/9pvi.fit
pddf	/app/data/pr_computation/pv/9pvi/9pvi.pr.out
profile	/app/data/saxs_computation/pv/9pvi/9pvi.dat