SAXSdb — 9bbw

▼

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	N-{(2R)-1-imino-3-[(3R)-2-oxopyrrolidin-3-yl]propan-2-yl}-N~2~-[4-(6-methoxypyridin-3-yl)benzoyl]-L-leucinamide × 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9bbw
Deposition date deposition_date	2024-04-07
Structure title title	SARS-CoV-2 Mpro in complex with compound 6k inhibitor
Keywords keywords	Protease, Inhibitor, VIRAL PROTEIN, Hydrolase; VIRAL PROTEIN, Hydrolase
Experimental Method method	X-RAY DIFFRACTION

▼

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.

9bbw__assembly_1__model_1

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

Download this curve (.dat)

9bbw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9bbw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.56 Å
Rg (electron density)	25.54 Å
Total Rg	26.40 Å
Atom count	4724
Residues	608
Excluded volume	83694 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9bbw__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	3C-like proteinase nsp5
Molecular weight formula_weight	33825.5 kDa
EC 编号 ec_number	3.4.22.69
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2405

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ

Source Source

Source organism organism	Severe acute respiratory syndrome coronavirus 2
NCBI taxonomy ID ncbi_taxonomy_id	2697049
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 non-polymer

Description description	N-{(2R)-1-imino-3-[(3R)-2-oxopyrrolidin-3-yl]propan-2-yl}-N~2~-[4-(6-methoxypyridin-3-yl)benzoyl]-L-leucinamide
Molecular weight formula_weight	479.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	43

▶

Unit-cell length a length_a	115.743 Å
Unit-cell length b length_b	53.776 Å
Unit-cell length c length_c	45.409 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.98 °
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	2.310 Å
Low-resolution limit resolution_low	48.580 Å
R factor r_factor	0.1977
R_work r_work	0.1940
R_free r_free	0.2309

SARS-CoV-2 Mpro in complex with compound 6k inhibitor

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

9bbw__assembly_1__model_1

9bbw__assembly_1__model_1 | I(q)

9bbw__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Citations (1)

SARS-CoV-2 Mpro in complex with compound 6k inhibitor

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

9bbw__assembly_1__model_1

9bbw__assembly_1__model_1 | I(q)

9bbw__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Citations (1)