SAXSdb — 9u7d

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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 homooligomer	Homooligomer	Protein 2	;(4~{a}~{S})-8-azanyl-3-methyl-~{N}-[1-[4-(oxan-4-ylamino)naphthalen-1-yl]cyclopropyl]-2,4,4~{a},5-tetrahydro-1~{H}-pyrazino[2,1-c][1,4]benzoxazine-9-carboxamide ; × 2 ZINC ION × 16 CHLORIDE ION × 12 DI(HYDROXYETHYL)ETHER × 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 1–312； UniProt 1564–1875

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	9u7d
Deposition date deposition_date	2025-03-24
Last revision last_revision	2025-12-24
Structure title title	Crystal structure of SARS-CoV-2 papain-like protease (Cys111Ser) in complex with YL1004
Keywords keywords	Severe acute respiratory syndrome coronavirus 2, papain-like protease, 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.

9u7d__assembly_1__model_1

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

Download this curve (.dat)

9u7d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9u7d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.92 Å
Rg (electron density)	28.03 Å
Total Rg	29.04 Å
Atom count	4990
Residues	614
Excluded volume	88898 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9u7d__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 (6)

Entity 1 Entity 1 polymer

Description description	Papain-like protease nsp3
Molecular weight formula_weight	35312.0 kDa
EC 编号 ec_number	3.4.19.12,3.4.22.-
Mutation mutation	C111S
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	2666

EVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNSYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTT

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	;(4~{a}~{S})-8-azanyl-3-methyl-~{N}-[1-[4-(oxan-4-ylamino)naphthalen-1-yl]cyclopropyl]-2,4,4~{a},5-tetrahydro-1~{H}-pyrazino[2,1-c][1,4]benzoxazine-9-carboxamide ;
Molecular weight formula_weight	527.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	165

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Unit-cell length a length_a	111.639 Å
Unit-cell length b length_b	111.639 Å
Unit-cell length c length_c	220.006 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	64.140 Å
R factor r_factor	0.2044
R_work r_work	0.2029
R_free r_free	0.2313

Crystal structure of SARS-CoV-2 papain-like protease (Cys111Ser) in complex with YL1004

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

9u7d__assembly_1__model_1

9u7d__assembly_1__model_1 | I(q)

9u7d__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

Crystal structure of SARS-CoV-2 papain-like protease (Cys111Ser) in complex with YL1004

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

9u7d__assembly_1__model_1

9u7d__assembly_1__model_1 | I(q)

9u7d__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)