SAXSdb — 9z0d

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

Papain-like protease nsp3

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 monomer	Monomer	Protein 1	ZINC ION × 1 ;N'-[3-(2-{[(7M)-8-methyl-7-(2-methylpyridin-4-yl)-3,4-dihydrospiro[[1]benzopyran-2,4'-piperidin]-1'-yl]methyl}pyridin-3-yl)propanoyl]-4-(2-oxa-6-azaspiro[3.3]heptan-6-yl)-4-oxobutanehydrazide ; × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 1 ;N'-[3-(2-{[(7M)-8-methyl-7-(2-methylpyridin-4-yl)-3,4-dihydrospiro[[1]benzopyran-2,4'-piperidin]-1'-yl]methyl}pyridin-3-yl)propanoyl]-4-(2-oxa-6-azaspiro[3.3]heptan-6-yl)-4-oxobutanehydrazide ; × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ZINC ION × 1 ;N'-[3-(2-{[(7M)-8-methyl-7-(2-methylpyridin-4-yl)-3,4-dihydrospiro[[1]benzopyran-2,4'-piperidin]-1'-yl]methyl}pyridin-3-yl)propanoyl]-4-(2-oxa-6-azaspiro[3.3]heptan-6-yl)-4-oxobutanehydrazide ; × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ZINC ION × 1 ;N'-[3-(2-{[(7M)-8-methyl-7-(2-methylpyridin-4-yl)-3,4-dihydrospiro[[1]benzopyran-2,4'-piperidin]-1'-yl]methyl}pyridin-3-yl)propanoyl]-4-(2-oxa-6-azaspiro[3.3]heptan-6-yl)-4-oxobutanehydrazide ; × 1 water × 1	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 5–319； UniProt 1564–1878 Author chain B； PDBConstruct 5–319； UniProt 1564–1878 Author chain C； PDBConstruct 5–319； UniProt 1564–1878 Author chain D； PDBConstruct 5–319； UniProt 1564–1878

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	9z0d
Deposition date deposition_date	2025-10-31
Structure title title	SARS-CoV-2 Papain-like Protease (PLpro) in complex with Fragment 41
Keywords keywords	Viral protease, Inhibitor, 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.

9z0d__assembly_1__model_1

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

Download this curve (.dat)

9z0d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9z0d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.76 Å
Rg (electron density)	23.08 Å
Total Rg	24.06 Å
Atom count	2494
Residues	312
Excluded volume	44158 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9z0d__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9z0d__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`9z0d__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`9z0d__assembly_4__model_1`	monomeric （1）	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	Papain-like protease nsp3
Molecular weight formula_weight	36000.8 kDa
EC 编号 ec_number	3.4.19.12,3.4.22.-
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	11285

GSNAEVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTIK

Source Source

Source organism organism	Severe acute respiratory syndrome coronavirus 2
NCBI taxonomy ID ncbi_taxonomy_id	2697049
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	;N'-[3-(2-{[(7M)-8-methyl-7-(2-methylpyridin-4-yl)-3,4-dihydrospiro[[1]benzopyran-2,4'-piperidin]-1'-yl]methyl}pyridin-3-yl)propanoyl]-4-(2-oxa-6-azaspiro[3.3]heptan-6-yl)-4-oxobutanehydrazide ;
Molecular weight formula_weight	666.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1102

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Unit-cell length a length_a	58.050 Å
Unit-cell length b length_b	63.190 Å
Unit-cell length c length_c	100.911 Å
Unit-cell angle α angle_alpha	107.36 °
Unit-cell angle β angle_beta	98.07 °
Unit-cell angle γ angle_gamma	98.22 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	47.250 Å
R factor r_factor	0.2015
R_work r_work	0.1996
R_free r_free	0.2383

SARS-CoV-2 Papain-like Protease (PLpro) in complex with Fragment 41

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

Papain-like protease nsp3

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

9z0d__assembly_1__model_1

9z0d__assembly_1__model_1 | I(q)

9z0d__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)

SARS-CoV-2 Papain-like Protease (PLpro) in complex with Fragment 41

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

Papain-like protease nsp3

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

9z0d__assembly_1__model_1

9z0d__assembly_1__model_1 | I(q)

9z0d__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)