← Back to search

9z6c

Crystal structure of SARS-CoV-2 PLpro in complex with compound 14

Method: X-RAY DIFFRACTION D_max: 88.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9z6c
deposition_date	2025-11-14
title	Crystal structure of SARS-CoV-2 PLpro in complex with compound 14
keywords	PLpro, papain-like protease, nsp3, 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	27.77 Å
rg_electron	26.91 Å
i0	161901000.00
molecular_weight	67793.0 kDa
excluded_volume	65732 Å³
envelope_volume	112000 Å³
shell_volume	34064 Å³
envelope_diameter	93.7 Å
shell_rg	34.89 Å
envelope_rg	27.05 Å
shape_rg	26.87 Å
total_rg	27.56 Å
total_atoms	5108
n_residues	634
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	88.8 Å
rg_real	27.65 Å
rg_real_error	0.59 Å
i0_real	1.6190e+08
i0_real_error	2.3770e+06
rg_reciprocal	27.69 Å
i0_reciprocal	161900000.0000
total_estimate	0.9020
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	34.3 Å
skewness	0.205
kurtosis	-0.440
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	15420000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.986

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

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	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5312

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	;methyl 4-{[(2E)-2-{[(2S)-3-amino-2-(1-{(1R)-1-[7-(propan-2-yl)naphthalen-1-yl]ethyl}piperidin-4-yl)propanoyl]imino}acetyl]amino}butanoate ;
formula_weight	522.7 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	204

▶

6. Citations (1)

▶

length_a	137.257 Å
length_b	161.630 Å
length_c	56.308 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	2.060 Å
resolution_low	69.640 Å
r_factor	0.2323
r_work	0.2319
r_free	0.2467

fit	/app/data/saxs_computation/z6/9z6c/9z6c.fit
pddf	/app/data/pr_computation/z6/9z6c/9z6c.pr.out
profile	/app/data/saxs_computation/z6/9z6c/9z6c.dat