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9z6b

Crystal structure of SARS-CoV-2 PLpro in complex with compound 10

Method: X-RAY DIFFRACTION D_max: 93.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z6b
deposition_date	2025-11-14
title	Crystal structure of SARS-CoV-2 PLpro in complex with compound 10
keywords	PLpro, papain-like protease, nsp3, 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	24.10 Å
rg_electron	23.66 Å
i0	42546700.00
molecular_weight	34013.0 kDa
excluded_volume	32968 Å³
envelope_volume	54881 Å³
shell_volume	20997 Å³
envelope_diameter	98.7 Å
shell_rg	28.71 Å
envelope_rg	24.50 Å
shape_rg	23.58 Å
total_rg	24.25 Å
total_atoms	2564
n_residues	319
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	93.7 Å
rg_real	24.38 Å
rg_real_error	1.05 Å
i0_real	4.2550e+07
i0_real_error	6.8820e+05
rg_reciprocal	24.32 Å
i0_reciprocal	42540000.0000
total_estimate	0.7607
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.4 Å
skewness	0.653
kurtosis	0.150
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	6136000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.501; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.423; Smooth: 0.959

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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	36039.9 kDa
ec_number	3.4.19.12,3.4.22.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2570

AEVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVT

Source

organism	Severe acute respiratory syndrome coronavirus 2
common_name	2019-nCoV, SARS-CoV-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	methyl 4-{[(2E)-2-{[(2S)-3-amino-2-{1-[(1R)-1-(naphthalen-1-yl)ethyl]piperidin-4-yl}propanoyl]imino}acetyl]amino}butanoate
formula_weight	480.6 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	6

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6. Citations (1)

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length_a	76.456 Å
length_b	114.779 Å
length_c	101.280 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	2.700 Å
resolution_low	63.630 Å
r_factor	0.2413
r_work	0.2403
r_free	0.2607

fit	/app/data/saxs_computation/z6/9z6b/9z6b.fit
pddf	/app/data/pr_computation/z6/9z6b/9z6b.pr.out
profile	/app/data/saxs_computation/z6/9z6b/9z6b.dat

Crystal structure of SARS-CoV-2 PLpro in complex with compound 10

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