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9z0c

SARS-CoV-2 Papain-like Protease (PLpro) in complex with Fragment 7

Method: X-RAY DIFFRACTION D_max: 85.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z0c
deposition_date	2025-10-31
title	SARS-CoV-2 Papain-like Protease (PLpro) in complex with Fragment 7
keywords	Viral protease, Inhibitor, 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	22.32 Å
rg_electron	21.85 Å
i0	34652800.00
molecular_weight	30826.0 kDa
excluded_volume	30053 Å³
envelope_volume	48473 Å³
shell_volume	19757 Å³
envelope_diameter	87.1 Å
shell_rg	27.18 Å
envelope_rg	22.39 Å
shape_rg	21.83 Å
total_rg	22.41 Å
total_atoms	2332
n_residues	297
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	85.8 Å
rg_real	22.47 Å
rg_real_error	0.79 Å
i0_real	3.4650e+07
i0_real_error	5.0540e+05
rg_reciprocal	22.44 Å
i0_reciprocal	34650000.0000
total_estimate	0.7877
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.4 Å
skewness	0.580
kurtosis	-0.012
angular_range	— – 0.3550 Å⁻¹
current_alpha	0.0000
highest_alpha	8548000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.528; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.652; Smooth: 1.000

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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.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2549

MREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNSYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQSGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPLEHHHHHH

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Escherichia coli

Entity 2 non-polymer

description	(7M)-1',8-dimethyl-7-(2-methylpyridin-4-yl)spiro[[1]benzopyran-2,4'-piperidin]-4(3H)-one
formula_weight	336.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

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

Entity 4 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	189

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6. Citations (1)

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length_a	77.784 Å
length_b	77.784 Å
length_c	231.185 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	1.900 Å
resolution_low	43.860 Å
r_factor	0.2103
r_work	0.2082
r_free	0.2518

fit	/app/data/saxs_computation/z0/9z0c/9z0c.fit
pddf	/app/data/pr_computation/z0/9z0c/9z0c.pr.out
profile	/app/data/saxs_computation/z0/9z0c/9z0c.dat