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9x7f

Crystal structure of PDCoV 3CL protease (3CLpro) in complex with compound 1

Method: X-RAY DIFFRACTION D_max: 132.0 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9x7f
deposition_date	2025-10-16
title	Crystal structure of PDCoV 3CL protease (3CLpro) in complex with compound 1
keywords	Protease, Mpro, Viral protein-inhibitor complex, 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	43.64 Å
rg_electron	43.26 Å
i0	1076000000.00
molecular_weight	181240.0 kDa
excluded_volume	175780 Å³
envelope_volume	326310 Å³
shell_volume	62805 Å³
envelope_diameter	136.6 Å
shell_rg	48.84 Å
envelope_rg	42.28 Å
shape_rg	43.24 Å
total_rg	43.47 Å
total_atoms	13685
n_residues	1756
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	132.0 Å
rg_real	43.50 Å
rg_real_error	1.02 Å
i0_real	1.0760e+09
i0_real_error	1.9980e+07
rg_reciprocal	43.63 Å
i0_reciprocal	1076000000.0000
total_estimate	0.6901
solution_quality	REASONABLE a REASONABLE solution
n_peaks	0
r_peak_primary	— Å
skewness	0.095
kurtosis	-0.763
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0000
highest_alpha	31770000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.977; Stabil: 1.000; Sysdev: 0.145; Positv: 1.000; Valcen: 1.000; Smooth: 0.602

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4. Crystallography & Experiment

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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	13761

AGIKILLHPSGVVERCMVSVVYNGSALNGIWLKNVVYCPRHVIGKFRGDQWTHMVSIADCRDFIVKCPIQGIQLNVQSVKMVGALLQLTVHTNNTATPDYKFERLQPGSSMTIACAYDGIVRHVYHVVLQLNNLIYASFLNGACGSVGYTLKGKTLYLHYMHHIEFNNKTHSGTDLEGNFYGPYVDEEVIQQQTAFQYYTDNVVAQLYAHLLTVDARPKWLAQSQISIEDFNSWAANNSFANFPCEQTNMSYIMGLSQTARVPVERILNTIIQLTTNRDGACIMGSYDFECDWTPEMVYNQ

Source

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

Entity 2 non-polymer

description	;(2~{S})-~{N}-[(2~{S})-1-azanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-2-[[(2~{S})-3,3-dimethyl-2-[2,2,2-tris(fluoranyl)ethanoylamino]butanoyl]amino]-4-methyl-pentanamide ;
formula_weight	477.5 kDa
src_method	syn
entity_count	6

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	76

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6. Citations (1)

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length_a	123.577 Å
length_b	123.577 Å
length_c	291.312 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	2.640 Å
resolution_low	53.510 Å
r_factor	0.2065
r_work	0.2045
r_free	0.2442

fit	/app/data/saxs_computation/x7/9x7f/9x7f.fit
pddf	/app/data/pr_computation/x7/9x7f/9x7f.pr.out
profile	/app/data/saxs_computation/x7/9x7f/9x7f.dat

Crystal structure of PDCoV 3CL protease (3CLpro) in complex with compound 1

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