SAXSdb — 7eo8

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

3C-like proteinase

Severe acute respiratory syndrome-related coronavirus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	2-[(1R)-4-methyl-1-oxidanyl-pent-3-enyl]-5,8-bis(oxidanyl)naphthalene-1,4-dione × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	R1A_CVHSA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–306； UniProt 3241–3546 Author chain B； PDBConstruct 1–306； UniProt 3241–3546

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	7eo8
Deposition date deposition_date	2021-04-21
Structure title title	Crystal structure of SARS coronavirus main protease in complex with an inhibitor Shikonin
Keywords keywords	SARS coronavirus main protease 3CL, 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.

7eo8__assembly_1__model_1

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

Download this curve (.dat)

7eo8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7eo8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.68 Å
Rg (electron density)	25.64 Å
Total Rg	26.42 Å
Atom count	4411
Residues	596
Excluded volume	78075 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7eo8__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 (2)

Entity 1 Entity 1 polymer

Description description	3C-like proteinase
Molecular weight formula_weight	33876.6 kDa
EC 编号 ec_number	3.4.22.69
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	4411

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIRKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGKFYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQCSGVTFQ

Source Source

Source organism organism	Severe acute respiratory syndrome-related coronavirus
Common name common_name	SARS-CoV
NCBI taxonomy ID ncbi_taxonomy_id	694009
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	2-[(1R)-4-methyl-1-oxidanyl-pent-3-enyl]-5,8-bis(oxidanyl)naphthalene-1,4-dione
Molecular weight formula_weight	288.3 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	7eo8A01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	7eo8A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1840 — main proteinase (3clpro) structure, domain 3
Homologous superfamily homologous superfamily	10 — main proteinase (3clpro) structure, domain 3

Domain ID domain_id	7eo8B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1840 — main proteinase (3clpro) structure, domain 3
Homologous superfamily homologous superfamily	10 — main proteinase (3clpro) structure, domain 3

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Unit-cell length a length_a	55.336 Å
Unit-cell length b length_b	60.620 Å
Unit-cell length c length_c	68.295 Å
Unit-cell angle α angle_alpha	90.94 °
Unit-cell angle β angle_beta	102.70 °
Unit-cell angle γ angle_gamma	108.62 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	2.281 Å
Low-resolution limit resolution_low	27.327 Å
R factor r_factor	0.2294
R_work r_work	0.2272
R_free r_free	0.2720

Crystal structure of SARS coronavirus main protease in complex with an inhibitor Shikonin

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

7eo8__assembly_1__model_1

7eo8__assembly_1__model_1 | I(q)

7eo8__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of SARS coronavirus main protease in complex with an inhibitor Shikonin

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

7eo8__assembly_1__model_1

7eo8__assembly_1__model_1 | I(q)

7eo8__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)