SAXSdb — 9paj

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

3C-like proteinase

Human coronavirus 229E

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	;(1R,2S,3S,6R,7S)-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-[(2S)-4,4,4-trifluoro-3,3-dimethyl-2-(2,2,2-trifluoroacetamido)butanoyl]-4-azatricyclo[5.2.1.0~2,6~]dec-8-ene-3-carboxamide (non-preferred name) ; × 2 DODECAETHYLENE GLYCOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	R1AB_CVH22
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–302； UniProt 2966–3267 Author chain B； PDBConstruct 1–302； UniProt 2966–3267

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	9paj
Deposition date deposition_date	2025-06-25
Last revision last_revision	2026-05-06
Structure title title	Crystal structure of HCoV-229E 3CLpro with ALG-0987655 (inhibitor 2)
Keywords keywords	HYDROLASE/INHIBITOR, HCoV 229E, Nsp5, ALG-097655, PAN CORONOVIRUS DRUG, INHIBITOR 2, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9paj__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9paj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9paj__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	26.25 Å
Rg (electron density)	25.30 Å
Total Rg	26.11 Å
Atom count	4802
Residues	603
Excluded volume	84068 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9paj__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	3C-like proteinase
Molecular weight formula_weight	33083.6 kDa
EC 编号 ec_number	3.4.22.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5395

AGLRKMAQPSGFVEKCVVRVCYGNTVLNGLWLGDIVYCPRHVIASNTTSAIDYDHEYSIMRLHNFSIISGTAFLGVVGATMHGVTLKIKVSQTNMHTPRHSFRTLKSGEGFNILACYDGCAQGVFGVNMRTNWTIRGSFINGACGSPGYNLKNGEVEFVYMHQIELGSGSHVGSSFDGVMYGGFEDQPNLQVESANQMLTVNVVAFLYAAILNGCTWWLKGEKLFVEHYNEWAQANGFTAMNGEDAFSILAAKTGVCVERLLHAIQVLNNGFGGKQILGYSSLNDEFSINEVVKQMFGVNLQ

Source Source

Source organism organism	Human coronavirus 229E
NCBI taxonomy ID ncbi_taxonomy_id	11137
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	;(1R,2S,3S,6R,7S)-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-[(2S)-4,4,4-trifluoro-3,3-dimethyl-2-(2,2,2-trifluoroacetamido)butanoyl]-4-azatricyclo[5.2.1.0~2,6~]dec-8-ene-3-carboxamide (non-preferred name) ;
Molecular weight formula_weight	579.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	DODECAETHYLENE GLYCOL
Molecular weight formula_weight	546.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	573

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Unit-cell length a length_a	53.311 Å
Unit-cell length b length_b	76.453 Å
Unit-cell length c length_c	76.840 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.44 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.320 Å
Low-resolution limit resolution_low	34.220 Å
R factor r_factor	0.1558
R_work r_work	0.1540
R_free r_free	0.1906

Crystal structure of HCoV-229E 3CLpro with ALG-0987655 (inhibitor 2)

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9paj__assembly_1__model_1

9paj__assembly_1__model_1 | I(q)

9paj__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Crystal structure of HCoV-229E 3CLpro with ALG-0987655 (inhibitor 2)

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9paj__assembly_1__model_1

9paj__assembly_1__model_1 | I(q)

9paj__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)