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13rd

PanDDA analysis group deposition -- Crystal structure of PLpro-C111S in complex with 3T-0366

Method: X-RAY DIFFRACTION D_max: 84.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	13rd
deposition_date	2025-09-17
last_revision	2026-02-18
title	PanDDA analysis group deposition -- Crystal structure of PLpro-C111S in complex with 3T-0366
keywords	PLpro, SARS-CoV-2, HYDROLASE; HYDROLASE
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	23.63 Å
rg_electron	23.11 Å
i0	40872600.00
molecular_weight	33222.0 kDa
excluded_volume	32158 Å³
envelope_volume	53257 Å³
shell_volume	20776 Å³
envelope_diameter	89.7 Å
shell_rg	28.43 Å
envelope_rg	23.50 Å
shape_rg	23.03 Å
total_rg	23.74 Å
total_atoms	2504
n_residues	313
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	84.4 Å
rg_real	23.83 Å
rg_real_error	0.85 Å
i0_real	4.0870e+07
i0_real_error	6.0890e+05
rg_reciprocal	23.78 Å
i0_reciprocal	40870000.0000
total_estimate	0.8257
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.7 Å
skewness	0.583
kurtosis	-0.031
angular_range	— – 0.3350 Å⁻¹
current_alpha	0.0000
highest_alpha	5976000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.690; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.709; Smooth: 0.957

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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	39803.1 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	2783

MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNSYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKHV

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	MALONATE ION
formula_weight	102.0 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	4-(4-methoxyphenyl)-1H-imidazole
formula_weight	174.2 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	279

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6. Citations (1)

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length_a	81.370 Å
length_b	81.370 Å
length_c	135.130 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 32 2 1
int_tables_number	154
crystal_system	trigonal

resolution	1.890 Å
resolution_low	26.630 Å
r_factor	0.1683
r_work	0.1669
r_free	0.1977

fit	/app/data/saxs_computation/3r/13rd/13rd.fit
pddf	/app/data/pr_computation/3r/13rd/13rd.pr.out
profile	/app/data/saxs_computation/3r/13rd/13rd.dat