SAXSdb — 8dkk

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

3C-like proteinase nsp5

Severe acute respiratory syndrome coronavirus 2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	R1AB_SARS2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–306； UniProt 3264–3569

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	8dkk
Deposition date deposition_date	2022-07-05
Structure title title	Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates
Keywords keywords	viral protein, HYDROLASE-HYDROLASE INHIBITOR complex, HYDROLASE, HYDROLASE-INHIBITOR complex; 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.

8dkk__assembly_1__model_1

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

Download this curve (.dat)

8dkk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8dkk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.42 Å
Rg (electron density)	25.36 Å
Total Rg	26.24 Å
Atom count	4738
Residues	612
Excluded volume	84249 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8dkk__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)

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	8dkkA01
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	8dkkA02
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	114.740 Å
Unit-cell length b length_b	54.490 Å
Unit-cell length c length_c	44.880 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	38.450 Å
R factor r_factor	0.2058
R_work r_work	0.2035
R_free r_free	0.2497

Description description	3C-like proteinase nsp5
Molecular weight formula_weight	33855.6 kDa
EC 编号 ec_number	3.4.22.69
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2504

Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates

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

3C-like proteinase nsp5

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

8dkk__assembly_1__model_1

8dkk__assembly_1__model_1 | I(q)

8dkk__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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Source organism organism	Severe acute respiratory syndrome coronavirus 2
Common name common_name	2019-nCoV, SARS-CoV-2
NCBI taxonomy ID ncbi_taxonomy_id	2697049
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	135

Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates

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

3C-like proteinase nsp5

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

8dkk__assembly_1__model_1

8dkk__assembly_1__model_1 | I(q)

8dkk__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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)