SAXSdb — 9x7i

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1. Protein Identity and Related Structures Protein Identity & Related Structures

3C-like protease

Canine coronavirus 2

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2881–3182 Chain C； UniProt 2881–3182	Not recorded	A1D7N (1~{R},2~{S},5~{S})-~{N}-[(2~{S})-1-azanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-3-[(2~{S})-3,3-dimethyl-2-(methylsulfonylamino)butanoyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；12% PEG3350, 100 mM sodium malonate, pH 5.0	Resolution 2.23 Å R-free 0.280
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 2881–3182 Chain D； UniProt 2881–3182	Not recorded	A1D7N (1~{R},2~{S},5~{S})-~{N}-[(2~{S})-1-azanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-3-[(2~{S})-3,3-dimethyl-2-(methylsulfonylamino)butanoyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；12% PEG3350, 100 mM sodium malonate, pH 5.0	Resolution 2.23 Å R-free 0.280
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 2881–3182 Chain H； UniProt 2881–3182	Not recorded	A1D7N (1~{R},2~{S},5~{S})-~{N}-[(2~{S})-1-azanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-3-[(2~{S})-3,3-dimethyl-2-(methylsulfonylamino)butanoyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；12% PEG3350, 100 mM sodium malonate, pH 5.0	Resolution 2.23 Å R-free 0.280
4	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 2881–3182 Chain G； UniProt 2881–3182	Not recorded	A1D7N (1~{R},2~{S},5~{S})-~{N}-[(2~{S})-1-azanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-3-[(2~{S})-3,3-dimethyl-2-(methylsulfonylamino)butanoyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；12% PEG3350, 100 mM sodium malonate, pH 5.0	Resolution 2.23 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9X7I	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9IR8 CCoV-HuPn-2018 3CL protease (3CLpro) in complex with compound 6 Deposited 2024-07-15	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2881–3182（302 aa） Chain D 2881–3182（302 aa）	Not recorded	A1D7M (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 × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；12% PEG3350, 100 mM sodium malonate, pH 5.0	Resolution 2.12 Å R-free 0.273
9IR8 CCoV-HuPn-2018 3CL protease (3CLpro) in complex with compound 6 Deposited 2024-07-15	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 2881–3182（302 aa） Chain C 2881–3182（302 aa）	Not recorded	A1D7M (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 × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；12% PEG3350, 100 mM sodium malonate, pH 5.0	Resolution 2.12 Å R-free 0.273
9UOP Crystal structure of CCoV-HuPn-2018 3CL protease (3CLpro) in complex with compound 8 Deposited 2025-04-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2881–3182（302 aa） Chain C 2881–3182（302 aa）	Not recorded	A1EPZ (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 × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% (w/v) PEG3350, 200 mM Lithium citrate tribasic tetrahydrate, pH8.4	Resolution 1.61 Å R-free 0.230
9UOP Crystal structure of CCoV-HuPn-2018 3CL protease (3CLpro) in complex with compound 8 Deposited 2025-04-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 2881–3182（302 aa） Chain D 2881–3182（302 aa）	Not recorded	A1EPZ (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 × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% (w/v) PEG3350, 200 mM Lithium citrate tribasic tetrahydrate, pH8.4	Resolution 1.61 Å R-free 0.230
9X7E Crystal of CCoV-HuPn-2018 3CL protease (3CLpro) in complex with nirmatrelvir Deposited 2025-10-16	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2881–3182（302 aa） Chain C 2881–3182（302 aa）	Not recorded	4WI (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 × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；12% PEG3350, 100 mM sodium malonate, pH 5.0	Resolution 2.37 Å R-free 0.300
9X7E Crystal of CCoV-HuPn-2018 3CL protease (3CLpro) in complex with nirmatrelvir Deposited 2025-10-16	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 2881–3182（302 aa） Chain F 2881–3182（302 aa）	Not recorded	4WI (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 × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；12% PEG3350, 100 mM sodium malonate, pH 5.0	Resolution 2.37 Å R-free 0.300
9X7E Crystal of CCoV-HuPn-2018 3CL protease (3CLpro) in complex with nirmatrelvir Deposited 2025-10-16	Different ligand/ion Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain D 2881–3182（302 aa） Chain G 2881–3182（302 aa）	Not recorded	4WI (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 × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；12% PEG3350, 100 mM sodium malonate, pH 5.0	Resolution 2.37 Å R-free 0.300
9X7E Crystal of CCoV-HuPn-2018 3CL protease (3CLpro) in complex with nirmatrelvir Deposited 2025-10-16	Different ligand/ion Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 2881–3182（302 aa） Chain H 2881–3182（302 aa）	Not recorded	4WI (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 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；12% PEG3350, 100 mM sodium malonate, pH 5.0	Resolution 2.37 Å R-free 0.300

3 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A8F2ZG71_9ALPC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–302； UniProt 2881–3182 Author chain B； PDBConstruct 1–302； UniProt 2881–3182 Author chain C； PDBConstruct 1–302； UniProt 2881–3182 Author chain D； PDBConstruct 1–302； UniProt 2881–3182 Author chain E； PDBConstruct 1–302； UniProt 2881–3182 Author chain F； PDBConstruct 1–302； UniProt 2881–3182 Author chain G； PDBConstruct 1–302； UniProt 2881–3182 Author chain H； PDBConstruct 1–302； UniProt 2881–3182

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9x7i
Deposition date deposition_date	2025-10-16
Structure title title	Crystal of CCoV-HuPn-2018 3CL protease (3CLpro) in complex with compound 3
Keywords keywords	Protease, Mpro, Viral protein-inhibitor complex, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	51.77 Å
Radius of gyration Rg (electron density) rg_electron	51.70 Å
Forward intensity I(0) i0	1769660000.00
Molecular weight molecular_weight	229100.0 kDa
Excluded volume excluded_volume	219930 Å³
Envelope volume envelope_volume	456590 Å³
Hydration-shell volume shell_volume	76162 Å³
Envelope diameter envelope_diameter	167.1 Å
Shell Rg shell_rg	52.03 Å
Envelope Rg envelope_rg	50.73 Å
Shape Rg shape_rg	51.70 Å
Total Rg total_rg	51.72 Å
Total atoms total_atoms	17253
Residues n_residues	2300
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	175.5 Å
Rg (real space) rg_real	51.81 Å
Rg uncertainty (real space) rg_real_error	2.22 Å
I(0) (real space) i0_real	1.7700e+09
I(0) uncertainty (real space) i0_real_error	3.9250e+07
Rg (reciprocal space) rg_reciprocal	51.72 Å
I(0) (reciprocal space) i0_reciprocal	1769000000.0000
Solution quality estimate total_estimate	0.8896
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	52.6 Å
Skewness Skewness skewness	0.255
Kurtosis Kurtosis kurtosis	-0.674
Angular range angular_range	— – 0.1500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	51570000.0000
Real-space data points n_real_points	31
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.874

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	3C-like protease
Molecular weight formula_weight	33037.3 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	17407

SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRVINYENEMSSVRLHNFSVSKNNVFLGVVSAKYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEGCPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVSENATLYFVYMHHLELGNGSHVGSNLEGEMYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFTELSSTDAFSMLAAKTGQSVEKLLDSIVRLNKGFGGRTILSYGSLCDEFTPTEVIRQMYGVNLQ

来源 Source

来源生物 organism	Canine coronavirus 2
NCBI Class编号 ncbi_taxonomy_id	2185079
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	;(1~{R},2~{S},5~{S})-~{N}-[(2~{S})-1-azanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-3-[(2~{S})-3,3-dimethyl-2-(methylsulfonylamino)butanoyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide ;
Molecular weight formula_weight	483.6 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	154

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8. Citations (1)

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Unit-cell length a length_a	159.119 Å
Unit-cell length b length_b	125.566 Å
Unit-cell length c length_c	158.604 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.76 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.230 Å
Low-resolution limit resolution_low	31.720 Å
R factor r_factor	0.2389
R_work r_work	0.2368
R_free r_free	0.2804

fit	/app/data/saxs_computation/x7/9x7i/9x7i.fit
pddf	/app/data/pr_computation/x7/9x7i/9x7i.pr.out
profile	/app/data/saxs_computation/x7/9x7i/9x7i.dat

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

3C-like protease

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction