← Back to search

9x7d

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

Method: X-RAY DIFFRACTION D_max: 139.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9x7d
deposition_date	2025-10-16
title	Crystal structure of PDCoV 3CL protease (3CLpro) in complex with nirmatrelvir
keywords	Protease, 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	42.46 Å
rg_electron	42.14 Å
i0	580161000.00
molecular_weight	197850.0 kDa
excluded_volume	246870 Å³
envelope_volume	319820 Å³
shell_volume	63277 Å³
envelope_diameter	143.3 Å
shell_rg	47.17 Å
envelope_rg	41.66 Å
shape_rg	42.11 Å
total_rg	42.50 Å
total_atoms	13923
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	139.0 Å
rg_real	42.40 Å
rg_real_error	1.62 Å
i0_real	5.8020e+08
i0_real_error	1.1880e+07
rg_reciprocal	42.46 Å
i0_reciprocal	580200000.0000
total_estimate	0.8971
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	48.8 Å
skewness	0.223
kurtosis	-0.559
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	44930000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.900

▶

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	14097

AGIKILLHPSGVVERCMVSVVYNGSALNGIWLKNVVYCPRHVIGKFRGDQWTHMVSIADCRDFIVKCPIQGIQLNVQSVKMVGALLQLTVHTNNTATPDYKFERLQPGSSMTIACAYDGIVRHVYHVVLQLNNLIYASFLNGACGSVGYTLKGKTLYLHYMHHIEFNNKTHSGTDLEGNFYGPYVDEEVIQQQTAFQYYTDNVVAQLYAHLLTVDARPKWLAQSQISIEDFNSWAANNSFANFPCEQTNMSYIMGLSQTARVPVERILNTIIQLTTNRDGACIMGSYDFECDWTPEMVYNQ

Source

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

Entity 2 non-polymer

description	;(1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide ;
formula_weight	501.5 kDa
src_method	syn
entity_count	6

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	174

▶

6. Citations (1)

▶

length_a	122.521 Å
length_b	122.521 Å
length_c	292.153 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	2.280 Å
resolution_low	61.260 Å
r_factor	0.2101
r_work	0.2082
r_free	0.2488

fit	/app/data/saxs_computation/x7/9x7d/9x7d.fit
pddf	/app/data/pr_computation/x7/9x7d/9x7d.pr.out
profile	/app/data/saxs_computation/x7/9x7d/9x7d.dat

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

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