7thh

SUD-C and Ubl2 domains of SARS CoV-2 Nsp3 protein

Method: X-RAY DIFFRACTION

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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	CHLORIDE ION × 2 HEXAETHYLENE GLYCOL × 1 1,2-ETHANEDIOL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	HEXAETHYLENE GLYCOL × 1 IODIDE ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	HEXAETHYLENE GLYCOL × 1 IODIDE ION × 2 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 2 1,2-ETHANEDIOL × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	CHLORIDE 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 4–131； UniProt 1496–1623 Author chain B； PDBConstruct 4–131； UniProt 1496–1623 Author chain C； PDBConstruct 4–131； UniProt 1496–1623 Author chain D； PDBConstruct 4–131； UniProt 1496–1623 Author chain E； PDBConstruct 4–131； UniProt 1496–1623 Author chain F； PDBConstruct 4–131； UniProt 1496–1623

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	7thh
Deposition date deposition_date	2022-01-11
Structure title title	SUD-C and Ubl2 domains of SARS CoV-2 Nsp3 protein
Keywords keywords	;Covid-19, coronavirus, SARS, CoV-2, nsp3, SARS coronavirus-unique domain, SUD-C, ubiquitin-like domain, Ubl2, CSGID-IDP51000, CSGID-IDP52003, Center for Structural Genomics of Infectious Diseases, CSGID, HYDROLASE, 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.

7thh__assembly_4__model_1

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

Download this curve (.dat)

7thh__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7thh__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	21.39 Å
Rg (electron density)	20.98 Å
Total Rg	21.62 Å
Atom count	1046
Residues	131
Excluded volume	18531 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7thh__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7thh__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`7thh__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`7thh__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`7thh__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`7thh__assembly_6__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 (6)

Entity 1 Entity 1 polymer

Description description	Papain-like protease nsp3
Molecular weight formula_weight	14815.5 kDa
EC 编号 ec_number	3.4.19.12,3.4.22.-
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	7374

SNATPEEHFIETISLAGSYKDWSYSGQSTQLGIEFLKRGDKSVYYTSNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPN

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(DE3)

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	HEXAETHYLENE GLYCOL
Molecular weight formula_weight	282.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	880

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	7thhA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	150 — Coronavirus polyprotein cleavage domain

Domain ID domain_id	7thhA02
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	7thhB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	150 — Coronavirus polyprotein cleavage domain

Domain ID domain_id	7thhB02
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	7thhC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	150 — Coronavirus polyprotein cleavage domain

Domain ID domain_id	7thhC02
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	7thhD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	150 — Coronavirus polyprotein cleavage domain

Domain ID domain_id	7thhD02
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	7thhE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	150 — Coronavirus polyprotein cleavage domain

Domain ID domain_id	7thhE02
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	7thhF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	150 — Coronavirus polyprotein cleavage domain

Domain ID domain_id	7thhF02
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

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Unit-cell length a length_a	30.173 Å
Unit-cell length b length_b	113.693 Å
Unit-cell length c length_c	109.688 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.02 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	1.320 Å
Low-resolution limit resolution_low	49.390 Å
R factor r_factor	0.1470
R_work r_work	0.1446
R_free r_free	0.1909

SUD-C and Ubl2 domains of SARS CoV-2 Nsp3 protein

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

7thh__assembly_4__model_1

7thh__assembly_4__model_1 | I(q)

7thh__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 (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

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

SUD-C and Ubl2 domains of SARS CoV-2 Nsp3 protein

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

7thh__assembly_4__model_1

7thh__assembly_4__model_1 | I(q)

7thh__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 (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

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)