SAXSdb — 9pae

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

3C-like proteinase

Human coronavirus OC43

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 3247–3549 Chain B； UniProt 3247–3549	Not recorded	A1CHF (1R,2R,3S,6S,7S)-4-[(2S)-3,3-dimethyl-2-(2,2,2-trifluoroacetamido)butanoyl]-10,10-difluoro-N-{(1E,2R)-1-imino-3-[(3R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl]propan-2-yl}-4-azatricyclo[5.2.1.0~2,6~]decane-3-carboxamide (non-preferred name) × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.2M Potassium thiocyanate, 0.1 M Bis-Tris pH 8.5 and 20% PEG3350	Resolution 2.31 Å R-free 0.280
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 3247–3549 Chain D； UniProt 3247–3549	Not recorded	A1CHF (1R,2R,3S,6S,7S)-4-[(2S)-3,3-dimethyl-2-(2,2,2-trifluoroacetamido)butanoyl]-10,10-difluoro-N-{(1E,2R)-1-imino-3-[(3R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl]propan-2-yl}-4-azatricyclo[5.2.1.0~2,6~]decane-3-carboxamide (non-preferred name) × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.2M Potassium thiocyanate, 0.1 M Bis-Tris pH 8.5 and 20% PEG3350	Resolution 2.31 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 9PAE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9C7W human OC43 Main Protease (1-303) in complex with potent inhibitor Deposited 2024-06-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3247–3544（298 aa）	Mutation：P3460L	A1AUY (8S)-3-(4,4-difluorocyclohexyl)-5-(pyrimidin-2-yl)pyrazolo[1,5-a]pyrimidine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1M HEPES pH 7.5, 8% EG, 10% PEG 8K	Resolution 2.08 Å R-free 0.246
9C7W human OC43 Main Protease (1-303) in complex with potent inhibitor Deposited 2024-06-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 3247–3544（298 aa）	Mutation：P3460L	A1AUY (8S)-3-(4,4-difluorocyclohexyl)-5-(pyrimidin-2-yl)pyrazolo[1,5-a]pyrimidine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1M HEPES pH 7.5, 8% EG, 10% PEG 8K	Resolution 2.08 Å R-free 0.246
9C7W human OC43 Main Protease (1-303) in complex with potent inhibitor Deposited 2024-06-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 3247–3544（298 aa）	Mutation：P3460L	A1AUY (8S)-3-(4,4-difluorocyclohexyl)-5-(pyrimidin-2-yl)pyrazolo[1,5-a]pyrimidine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1M HEPES pH 7.5, 8% EG, 10% PEG 8K	Resolution 2.08 Å R-free 0.246
9C7W human OC43 Main Protease (1-303) in complex with potent inhibitor Deposited 2024-06-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 3247–3544（298 aa）	Mutation：P3460L	A1AUY (8S)-3-(4,4-difluorocyclohexyl)-5-(pyrimidin-2-yl)pyrazolo[1,5-a]pyrimidine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1M HEPES pH 7.5, 8% EG, 10% PEG 8K	Resolution 2.08 Å R-free 0.246
9Y8X OC43 Mpro with EGT710 Deposited 2025-09-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 3247–3549（303 aa）	Not recorded	A1CBU (4S)-4-(iminomethyl)-3-(isoquinolin-4-yl)-1-[6-(trifluoromethyl)pyridin-3-yl]imidazolidin-2-one × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.2M NaSCN, 30% Peg 3350	Resolution 2.12 Å R-free 0.265

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

View Construct and Data Evidence

UniProt name	U3M6R3_CVHOC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–303； UniProt 3247–3549 Author chain B； PDBConstruct 1–303； UniProt 3247–3549 Author chain C； PDBConstruct 1–303； UniProt 3247–3549 Author chain D； PDBConstruct 1–303； UniProt 3247–3549

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	9pae
Deposition date deposition_date	2025-06-25
Structure title title	Crystal structure of HCoV OC43 3CLpro with ALG-097608 (inhibitor 1)
Keywords keywords	HYDROLASE/inhibitor, 3CL Protease, Nsp5, Pan coronavirus, ALG-097608, INHIBITOR 1, 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	37.35 Å
Radius of gyration Rg (electron density) rg_electron	37.19 Å
Forward intensity I(0) i0	541948000.00
Molecular weight molecular_weight	126690.0 kDa
Excluded volume excluded_volume	122730 Å³
Envelope volume envelope_volume	215910 Å³
Hydration-shell volume shell_volume	49476 Å³
Envelope diameter envelope_diameter	134.0 Å
Shell Rg shell_rg	42.17 Å
Envelope Rg envelope_rg	36.85 Å
Shape Rg shape_rg	37.14 Å
Total Rg total_rg	37.51 Å
Total atoms total_atoms	9528
Residues n_residues	1212
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	127.0 Å
Rg (real space) rg_real	37.52 Å
Rg uncertainty (real space) rg_real_error	1.08 Å
I(0) (real space) i0_real	5.4190e+08
I(0) uncertainty (real space) i0_real_error	9.5850e+06
Rg (reciprocal space) rg_reciprocal	37.42 Å
I(0) (reciprocal space) i0_reciprocal	541900000.0000
Solution quality estimate total_estimate	0.8657
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	42.3 Å
Skewness Skewness skewness	0.476
Kurtosis Kurtosis kurtosis	-0.211
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	30010000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.821; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.802

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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 proteinase
Molecular weight formula_weight	33503.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9953

SGIVKMVNPTSKVEPCVVSVTYGNMTLNGLWLDDKVYCPRHVICSASDMTNPDYTNLLCRVTSSDFTVLFDRLSLTVMSYQMRGCMLVLTVTLQNSRTPKYTFGVVKPGETFTVLAAYNGKPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVIMGDCVKFVYMHQLELSTGCHTGTDFNGDFYGPYKDAQVVQLLIQDYIQSVNFVAWLYAAILNNCNWFVQSDKCSVEDFNVWALSNGFSQVKSDLVIDALASMTGVSLETLLAAIKRLKNGFQGRQIMGSCSFEDELTPSDVYQQLAGIKLQ

来源 Source

来源生物 organism	Human coronavirus OC43
NCBI Class编号 ncbi_taxonomy_id	31631
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	;(1R,2R,3S,6S,7S)-4-[(2S)-3,3-dimethyl-2-(2,2,2-trifluoroacetamido)butanoyl]-10,10-difluoro-N-{(1E,2R)-1-imino-3-[(3R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl]propan-2-yl}-4-azatricyclo[5.2.1.0~2,6~]decane-3-carboxamide (non-preferred name) ;
Molecular weight formula_weight	561.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	413

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8. Citations (1)

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Unit-cell length a length_a	164.087 Å
Unit-cell length b length_b	106.499 Å
Unit-cell length c length_c	107.309 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	127.55 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.310 Å
Low-resolution limit resolution_low	33.960 Å
R factor r_factor	0.2172
R_work r_work	0.2140
R_free r_free	0.2803

fit	/app/data/saxs_computation/pa/9pae/9pae.fit
pddf	/app/data/pr_computation/pa/9pae/9pae.pr.out
profile	/app/data/saxs_computation/pa/9pae/9pae.dat

Crystal structure of HCoV OC43 3CLpro with ALG-097608 (inhibitor 1)

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

3C-like proteinase

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