SAXSdb — 6wuu

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

Non-structural protein 3

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 heterocomplex	Heteromer	Protein 2	VIR250 × 1 ZINC ION × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	VIR250 × 1 ZINC ION × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	VIR250 × 1 ZINC ION × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	VIR250 × 1 ZINC ION × 1 MAGNESIUM ION × 2 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 2–318； UniProt 1563–1879 Author chain B； PDBConstruct 2–318； UniProt 1563–1879 Author chain C； PDBConstruct 2–318； UniProt 1563–1879 Author chain D； PDBConstruct 2–318； UniProt 1563–1879

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	6wuu
Deposition date deposition_date	2020-05-05
Structure title title	Crystal structure of the SARS CoV-2 Papain-like protease in complex with peptide inhibitor VIR250
Keywords keywords	;COVID-19, CORONAVIRUS, SARS, COV-2, PAPAIN-LIKE PROTEASE, PLpro, deubiquitinating enzyme, ubiquitin, activity-based probe, Hydrolase-Hydrolase Inhibitor complex ;; Hydrolase/Hydrolase Inhibitor
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.

6wuu__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6wuu__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6wuu__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	24.64 Å
Rg (electron density)	24.15 Å
Total Rg	25.07 Å
Atom count	2564
Residues	319
Excluded volume	45755 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6wuu__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6wuu__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6wuu__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6wuu__assembly_4__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 (5)

Entity 1 Entity 1 polymer

Description description	Non-structural protein 3
Molecular weight formula_weight	37128.1 kDa
EC 编号 ec_number	3.4.19.121, 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	10292

MREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPLEHHHHHH

Source Source

Source organism organism	Severe acute respiratory syndrome coronavirus 2
Common name common_name	2019-nCoV
NCBI taxonomy ID ncbi_taxonomy_id	2697049
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	VIR250
Molecular weight formula_weight	504.6 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I,J

XXAGX

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	4

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	18

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	6wuuA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	540 — Papain-like viral protease, N-terminal domain

Domain ID domain_id	6wuuA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	1190 — Papain-like viral protease, thumb domain

Domain ID domain_id	6wuuA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	1680 —

Domain ID domain_id	6wuuB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	540 — Papain-like viral protease, N-terminal domain

Domain ID domain_id	6wuuB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	1190 — Papain-like viral protease, thumb domain

Domain ID domain_id	6wuuB03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	1680 —

Domain ID domain_id	6wuuC01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	540 — Papain-like viral protease, N-terminal domain

Domain ID domain_id	6wuuC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	1190 — Papain-like viral protease, thumb domain

Domain ID domain_id	6wuuC03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	1680 —

Domain ID domain_id	6wuuD01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	540 — Papain-like viral protease, N-terminal domain

Domain ID domain_id	6wuuD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	1190 — Papain-like viral protease, thumb domain

Domain ID domain_id	6wuuD03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	1680 —

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Unit-cell length a length_a	58.425 Å
Unit-cell length b length_b	189.693 Å
Unit-cell length c length_c	63.118 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.66 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.790 Å
Low-resolution limit resolution_low	94.850 Å
R factor r_factor	0.1973
R_work r_work	0.1952
R_free r_free	0.2297

Crystal structure of the SARS CoV-2 Papain-like protease in complex with peptide inhibitor VIR250

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

Non-structural protein 3

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

6wuu__assembly_4__model_1

6wuu__assembly_4__model_1 | I(q)

6wuu__assembly_4__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (2)

Crystal structure of the SARS CoV-2 Papain-like protease in complex with peptide inhibitor VIR250

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

Non-structural protein 3

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

6wuu__assembly_4__model_1

6wuu__assembly_4__model_1 | I(q)

6wuu__assembly_4__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (2)