← Back to search

9u7d

Crystal structure of SARS-CoV-2 papain-like protease (Cys111Ser) in complex with YL1004

Method: X-RAY DIFFRACTION D_max: 84.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9u7d
deposition_date	2025-03-24
last_revision	2025-12-24
title	Crystal structure of SARS-CoV-2 papain-like protease (Cys111Ser) in complex with YL1004
keywords	Severe acute respiratory syndrome coronavirus 2, papain-like protease, 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	23.22 Å
rg_electron	22.62 Å
i0	42371400.00
molecular_weight	33589.0 kDa
excluded_volume	32303 Å³
envelope_volume	53336 Å³
shell_volume	20931 Å³
envelope_diameter	86.2 Å
shell_rg	28.34 Å
envelope_rg	23.20 Å
shape_rg	22.54 Å
total_rg	23.27 Å
total_atoms	2495
n_residues	307
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	84.5 Å
rg_real	23.37 Å
rg_real_error	0.81 Å
i0_real	4.2370e+07
i0_real_error	6.2350e+05
rg_reciprocal	23.33 Å
i0_reciprocal	42370000.0000
total_estimate	0.8276
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.7 Å
skewness	0.555
kurtosis	-0.053
angular_range	— – 0.3400 Å⁻¹
current_alpha	0.0000
highest_alpha	5133000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.667; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.771; Smooth: 0.983

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

Entity 1 polymer

description	Papain-like protease nsp3
formula_weight	35312.0 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	2666

EVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNSYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTT

Source

organism	Severe acute respiratory syndrome coronavirus 2
common_name	2019-nCoV, SARS-CoV-2
ncbi_taxonomy_id	2697049
host_organism	Escherichia coli

Entity 2 non-polymer

description	;(4~{a}~{S})-8-azanyl-3-methyl-~{N}-[1-[4-(oxan-4-ylamino)naphthalen-1-yl]cyclopropyl]-2,4,4~{a},5-tetrahydro-1~{H}-pyrazino[2,1-c][1,4]benzoxazine-9-carboxamide ;
formula_weight	527.7 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	8

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	6

Entity 5 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	165

▶

6. Citations (1)

▶

length_a	111.639 Å
length_b	111.639 Å
length_c	220.006 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	I 41 2 2
int_tables_number	98
crystal_system	—

resolution	2.700 Å
resolution_low	64.140 Å
r_factor	0.2044
r_work	0.2029
r_free	0.2313

fit	/app/data/saxs_computation/u7/9u7d/9u7d.fit
pddf	/app/data/pr_computation/u7/9u7d/9u7d.pr.out
profile	/app/data/saxs_computation/u7/9u7d/9u7d.dat