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9x7e

Crystal of CCoV-HuPn-2018 3CL protease (3CLpro) in complex with nirmatrelvir

Method: X-RAY DIFFRACTION D_max: 145.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9x7e
deposition_date	2025-10-16
title	Crystal of CCoV-HuPn-2018 3CL protease (3CLpro) in complex with nirmatrelvir
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	45.64 Å
rg_electron	45.28 Å
i0	811311000.00
molecular_weight	223370.0 kDa
excluded_volume	274070 Å³
envelope_volume	409620 Å³
shell_volume	75918 Å³
envelope_diameter	145.9 Å
shell_rg	49.18 Å
envelope_rg	44.65 Å
shape_rg	45.30 Å
total_rg	45.39 Å
total_atoms	15728
n_residues	2238
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	145.1 Å
rg_real	45.45 Å
rg_real_error	1.15 Å
i0_real	8.1130e+08
i0_real_error	1.5710e+07
rg_reciprocal	45.64 Å
i0_reciprocal	811500000.0000
total_estimate	0.8971
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	58.0 Å
skewness	0.164
kurtosis	-0.496
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	47980000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.866

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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	33037.3 kDa
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H
atom_count	15769

SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSAKYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVSENATLYFVYMHHLELGNGSHVGSNLEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGVNLQ

Source

organism	Canine coronavirus 2
ncbi_taxonomy_id	2185079
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	7

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	41

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6. Citations (1)

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length_a	159.988 Å
length_b	126.453 Å
length_c	159.802 Å
angle_alpha	90.00 °
angle_beta	90.82 °
angle_gamma	90.00 °
z_pdb	32

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.370 Å
resolution_low	38.670 Å
r_factor	0.2648
r_work	0.2628
r_free	0.3003

fit	/app/data/saxs_computation/x7/9x7e/9x7e.fit
pddf	/app/data/pr_computation/x7/9x7e/9x7e.pr.out
profile	/app/data/saxs_computation/x7/9x7e/9x7e.dat

Crystal of CCoV-HuPn-2018 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