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13qd

PanDDA analysis group deposition -- Crystal structure of PLpro-C111S in complex with Fr13673

Method: X-RAY DIFFRACTION D_max: 85.4 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	13qd
deposition_date	2025-09-17
last_revision	2026-02-18
title	PanDDA analysis group deposition -- Crystal structure of PLpro-C111S in complex with Fr13673
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	23.66 Å
rg_electron	23.15 Å
i0	41613700.00
molecular_weight	33461.0 kDa
excluded_volume	32371 Å³
envelope_volume	53626 Å³
shell_volume	20807 Å³
envelope_diameter	89.8 Å
shell_rg	28.43 Å
envelope_rg	23.65 Å
shape_rg	23.07 Å
total_rg	23.77 Å
total_atoms	2518
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	85.4 Å
rg_real	23.86 Å
rg_real_error	0.83 Å
i0_real	4.1610e+07
i0_real_error	6.0480e+05
rg_reciprocal	23.82 Å
i0_reciprocal	41610000.0000
total_estimate	0.6550
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	24.0 Å
skewness	0.584
kurtosis	-0.024
angular_range	— – 0.3350 Å⁻¹
current_alpha	0.0000
highest_alpha	6397000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.677; Stabil: 1.000; Sysdev: 0.286; Positv: 1.000; Valcen: 0.687; Smooth: 0.936

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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	2794

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-methylthiophene-2-carboxamide
formula_weight	141.2 kDa
src_method	syn
entity_count	3

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	276

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6. Citations (1)

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length_a	82.710 Å
length_b	82.710 Å
length_c	134.270 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	1.920 Å
resolution_low	35.210 Å
r_factor	0.1679
r_work	0.1671
r_free	0.1830

fit	/app/data/saxs_computation/3q/13qd/13qd.fit
pddf	/app/data/pr_computation/3q/13qd/13qd.pr.out
profile	/app/data/saxs_computation/3q/13qd/13qd.dat