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9puj

SARS-CoV-2 Papain-like Protease (PLpro) in complex with Fragment 17

Method: X-RAY DIFFRACTION D_max: 75.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9puj
deposition_date	2025-07-31
title	SARS-CoV-2 Papain-like Protease (PLpro) in complex with Fragment 17
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	22.54 Å
rg_electron	21.83 Å
i0	36724100.00
molecular_weight	31698.0 kDa
excluded_volume	30808 Å³
envelope_volume	50354 Å³
shell_volume	20258 Å³
envelope_diameter	78.8 Å
shell_rg	27.95 Å
envelope_rg	22.11 Å
shape_rg	21.75 Å
total_rg	22.55 Å
total_atoms	2391
n_residues	307
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	75.2 Å
rg_real	22.61 Å
rg_real_error	0.41 Å
i0_real	3.6720e+07
i0_real_error	4.9970e+05
rg_reciprocal	22.59 Å
i0_reciprocal	36720000.0000
total_estimate	0.8856
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.9 Å
skewness	0.419
kurtosis	-0.361
angular_range	— – 0.3500 Å⁻¹
current_alpha	0.0002
highest_alpha	4855000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.858; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.990

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Papain-like protease nsp3
formula_weight	37812.7 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	2577

MGSSHHHHHHSSGLVPRGSHMEVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNSYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQSGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTI

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	1'-methylspiro[naphtho[1,2-b]pyran-2,4'-piperidin]-4(3H)-one
formula_weight	281.3 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	186

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6. Citations (1)

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length_a	102.548 Å
length_b	102.548 Å
length_c	139.948 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 61 2 2
int_tables_number	178
crystal_system	hexagonal

resolution	2.000 Å
resolution_low	29.600 Å
r_factor	0.1989
r_work	0.1971
r_free	0.2344

fit	/app/data/saxs_computation/pu/9puj/9puj.fit
pddf	/app/data/pr_computation/pu/9puj/9puj.pr.out
profile	/app/data/saxs_computation/pu/9puj/9puj.dat

SARS-CoV-2 Papain-like Protease (PLpro) in complex with Fragment 17

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