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9puh

SARS-CoV-2 Papain-like Protease (PLpro) in complex with Fragment 11

Method: X-RAY DIFFRACTION D_max: 125.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9puh
deposition_date	2025-07-31
title	SARS-CoV-2 Papain-like Protease (PLpro) in complex with Fragment 11
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	32.61 Å
rg_electron	32.19 Å
i0	317137000.00
molecular_weight	96057.0 kDa
excluded_volume	93171 Å³
envelope_volume	164630 Å³
shell_volume	43383 Å³
envelope_diameter	132.4 Å
shell_rg	38.37 Å
envelope_rg	32.61 Å
shape_rg	32.19 Å
total_rg	32.55 Å
total_atoms	7241
n_residues	941
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	125.6 Å
rg_real	32.66 Å
rg_real_error	1.36 Å
i0_real	3.1710e+08
i0_real_error	5.7450e+06
rg_reciprocal	32.64 Å
i0_reciprocal	317100000.0000
total_estimate	0.8164
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	38.5 Å
skewness	0.449
kurtosis	0.060
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	26870000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.572; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.899; Smooth: 0.994

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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	35923.7 kDa
ec_number	3.4.19.12,3.4.22.-
mutation	C111S
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	D,A,B
atom_count	7532

GSHMEVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNSYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQSGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTI

Source

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

Entity 2 non-polymer

description	1'-methylspiro[[1]benzopyran-2,4'-piperidin]-4(3H)-one
formula_weight	231.3 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	3

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	291

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6. Citations (1)

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length_a	99.553 Å
length_b	101.987 Å
length_c	128.375 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	12

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.390 Å
resolution_low	35.620 Å
r_factor	0.1944
r_work	0.1925
r_free	0.2445

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

SARS-CoV-2 Papain-like Protease (PLpro) in complex with Fragment 11

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