← Back to search

9z0d

SARS-CoV-2 Papain-like Protease (PLpro) in complex with Fragment 41

Method: X-RAY DIFFRACTION D_max: 128.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9z0d
deposition_date	2025-10-31
title	SARS-CoV-2 Papain-like Protease (PLpro) in complex with Fragment 41
keywords	Viral protease, Inhibitor, VIRAL PROTEIN; VIRAL PROTEIN
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	36.95 Å
rg_electron	36.75 Å
i0	592537000.00
molecular_weight	132610.0 kDa
excluded_volume	128740 Å³
envelope_volume	228350 Å³
shell_volume	52805 Å³
envelope_diameter	136.6 Å
shell_rg	41.64 Å
envelope_rg	36.70 Å
shape_rg	36.78 Å
total_rg	36.95 Å
total_atoms	9993
n_residues	1257
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

▼

3. P(r) Analysis (GNOM)

dmax	128.4 Å
rg_real	37.12 Å
rg_real_error	1.32 Å
i0_real	5.9250e+08
i0_real_error	1.0280e+07
rg_reciprocal	37.02 Å
i0_reciprocal	592500000.0000
total_estimate	0.8422
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	41.8 Å
skewness	0.538
kurtosis	-0.026
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	40060000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.725; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.824

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	Papain-like protease nsp3
formula_weight	36000.8 kDa
ec_number	3.4.19.12,3.4.22.-
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	11285

GSNAEVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTIK

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	4

Entity 3 non-polymer

description	;N'-[3-(2-{[(7M)-8-methyl-7-(2-methylpyridin-4-yl)-3,4-dihydrospiro[[1]benzopyran-2,4'-piperidin]-1'-yl]methyl}pyridin-3-yl)propanoyl]-4-(2-oxa-6-azaspiro[3.3]heptan-6-yl)-4-oxobutanehydrazide ;
formula_weight	666.8 kDa
src_method	syn
entity_count	4

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1102

▶

6. Citations (1)

▶

length_a	58.050 Å
length_b	63.190 Å
length_c	100.911 Å
angle_alpha	107.36 °
angle_beta	98.07 °
angle_gamma	98.22 °
z_pdb	4

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	1.650 Å
resolution_low	47.250 Å
r_factor	0.2015
r_work	0.1996
r_free	0.2383

fit	/app/data/saxs_computation/z0/9z0d/9z0d.fit
pddf	/app/data/pr_computation/z0/9z0d/9z0d.pr.out
profile	/app/data/saxs_computation/z0/9z0d/9z0d.dat

SARS-CoV-2 Papain-like Protease (PLpro) in complex with Fragment 41

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