← Back to search

9uos

Crystal structure of PDCoV 3CL protease (3CLpro) in complex with compound 8

Method: X-RAY DIFFRACTION D_max: 136.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9uos
deposition_date	2025-04-26
title	Crystal structure of PDCoV 3CL protease (3CLpro) in complex with compound 8
keywords	Mpro, VIRAL PROTEIN-inhibitor complex, 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	42.36 Å
rg_electron	42.06 Å
i0	1095740000.00
molecular_weight	182190.0 kDa
excluded_volume	176630 Å³
envelope_volume	319070 Å³
shell_volume	63175 Å³
envelope_diameter	139.8 Å
shell_rg	46.96 Å
envelope_rg	41.60 Å
shape_rg	42.04 Å
total_rg	42.27 Å
total_atoms	13756
n_residues	1767
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	136.7 Å
rg_real	42.30 Å
rg_real_error	1.14 Å
i0_real	1.0960e+09
i0_real_error	1.8390e+07
rg_reciprocal	42.36 Å
i0_reciprocal	1096000000.0000
total_estimate	0.8941
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	48.0 Å
skewness	0.223
kurtosis	-0.567
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	40480000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.800

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	3C-like protease
formula_weight	33972.6 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	13778

AGIKILLHPSGVVERCMVSVVYNGSALNGIWLKNVVYCPRHVIGKFRGDQWTHMVSIADCRDFIVKCPIQGIQLNVQSVKMVGALLQLTVHTNNTATPDYKFERLQPGSSMTIACAYDGIVRHVYHVVLQLNNLIYASFLNGACGSVGYTLKGKTLYLHYMHHIEFNNKTHSGTDLEGNFYGPYVDEEVIQQQTAFQYYTDNVVAQLYAHLLTVDARPKWLAQSQISIEDFNSWAANNSFANFPCEQTNMSYIMGLSQTARVPVERILNTIIQLTTNRDGACIMGSYDFECDWTPEMVYNQ

Source

organism	Porcine deltacoronavirus
ncbi_taxonomy_id	1586324
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	;(2~{S})-2-[[(2~{S})-3,3-dimethyl-2-[2,2,2-tris(fluoranyl)ethanoylamino]butanoyl]amino]-4-methyl-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]pentanamide ;
formula_weight	478.5 kDa
src_method	syn
entity_count	6

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	22

▶

6. Citations (1)

▶

length_a	122.820 Å
length_b	122.820 Å
length_c	290.907 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	36

space_group	P 61
int_tables_number	169
crystal_system	—

resolution	2.730 Å
resolution_low	61.410 Å
r_factor	0.2245
r_work	0.2227
r_free	0.2595

fit	/app/data/saxs_computation/uo/9uos/9uos.fit
pddf	/app/data/pr_computation/uo/9uos/9uos.pr.out
profile	/app/data/saxs_computation/uo/9uos/9uos.dat

Crystal structure of PDCoV 3CL protease (3CLpro) in complex with compound 8

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