9x7h

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

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

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

3C-like protease

Porcine deltacoronavirus

UniProt A0A166XB12

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 2509–2809 Chain B; UniProt 2509–2809 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, HANGING DROP;293 K;0.5-2% PEG6000, 100 mM sodium citrate, pH 4.6-5.25 Resolution 2.56 Å R-free 0.244
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 2509–2809 Chain D; UniProt 2509–2809 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, HANGING DROP;293 K;0.5-2% PEG6000, 100 mM sodium citrate, pH 4.6-5.25 Resolution 2.56 Å R-free 0.244
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 2509–2809 Chain F; UniProt 2509–2809 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, HANGING DROP;293 K;0.5-2% PEG6000, 100 mM sodium citrate, pH 4.6-5.25 Resolution 2.56 Å R-free 0.244

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.

5 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A166XB12_9NIDO
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–301; UniProt 2509–2809 Author chain B; PDBConstruct 1–301; UniProt 2509–2809 Author chain C; PDBConstruct 1–301; UniProt 2509–2809 Author chain D; PDBConstruct 1–301; UniProt 2509–2809 Author chain E; PDBConstruct 1–301; UniProt 2509–2809 Author chain F; PDBConstruct 1–301; UniProt 2509–2809

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.

SAXS scattering curve SAXS Profile

SAXS profile for 9x7h

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9x7h
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9x7h
Deposition date deposition_date2025-10-16
Structure title titleCrystal structure of PDCoV 3CL protease (3CLpro) in complex with compound 6
Keywords keywordsProtease, Mpro, Viral protein-inhibitor complex, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier42.47
Radius of gyration Rg (electron density) rg_electron42.16
Forward intensity I(0) i01154530000.00
Molecular weight molecular_weight186110.0 kDa
Excluded volume excluded_volume179980 ų
Envelope volume envelope_volume323560 ų
Hydration-shell volume shell_volume64562 ų
Envelope diameter envelope_diameter148.3
Shell Rg shell_rg46.71
Envelope Rg envelope_rg41.70
Shape Rg shape_rg42.14
Total Rg total_rg42.36
Total atoms total_atoms14052
Residues n_residues1767
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax140.3
Rg (real space) rg_real42.44
Rg uncertainty (real space) rg_real_error1.57
I(0) (real space) i0_real1.1550e+09
I(0) uncertainty (real space) i0_real_error2.1440e+07
Rg (reciprocal space) rg_reciprocal42.47
I(0) (reciprocal space) i0_reciprocal1155000000.0000
Solution quality estimate total_estimate0.8917
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary45.5
Skewness Skewness skewness0.288
Kurtosis Kurtosis kurtosis-0.459
Angular range angular_range— – 0.1850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha42370000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.904; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.882

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)