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9x7h

Crystal structure of PDCoV 3CL protease (3CLpro) in complex with compound 6

Method: X-RAY DIFFRACTION D_max: 140.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9x7h
deposition_date	2025-10-16
title	Crystal structure of PDCoV 3CL protease (3CLpro) in complex with compound 6
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	42.47 Å
rg_electron	42.16 Å
i0	1154530000.00
molecular_weight	186110.0 kDa
excluded_volume	179980 Å³
envelope_volume	323560 Å³
shell_volume	64562 Å³
envelope_diameter	148.3 Å
shell_rg	46.71 Å
envelope_rg	41.70 Å
shape_rg	42.14 Å
total_rg	42.36 Å
total_atoms	14052
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

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3. P(r) Analysis (GNOM)

dmax	140.3 Å
rg_real	42.44 Å
rg_real_error	1.57 Å
i0_real	1.1550e+09
i0_real_error	2.1440e+07
rg_reciprocal	42.47 Å
i0_reciprocal	1155000000.0000
total_estimate	0.8917
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	45.5 Å
skewness	0.288
kurtosis	-0.459
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	42370000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.882

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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	14164

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-(methylsulfonylamino)butanoyl]amino]-4-methyl-pentanamide ;
formula_weight	459.6 kDa
src_method	syn
entity_count	6

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	112

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6. Citations (1)

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length_a	122.926 Å
length_b	122.926 Å
length_c	291.591 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	2.560 Å
resolution_low	53.230 Å
r_factor	0.2007
r_work	0.1983
r_free	0.2439

fit	/app/data/saxs_computation/x7/9x7h/9x7h.fit
pddf	/app/data/pr_computation/x7/9x7h/9x7h.pr.out
profile	/app/data/saxs_computation/x7/9x7h/9x7h.dat

Crystal structure of PDCoV 3CL protease (3CLpro) in complex with compound 6

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