7THH

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

PDB DOI: https://doi.org/10.2210/pdb7THH/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-01-11 Released: 2022-01-19
Deposition Author(s): Osipiuk, J., Jedrzejczak, R., Endres, M., Wydorski, P., Joachimiak, L., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.32 Å
R-Value Free: 0.191
R-Value Work: 0.145
R-Value Observed: 0.147

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

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

Osipiuk, J., Jedrzejczak, R., Endres, M., Wydorski, P., Joachimiak, L., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 90.46 kDa
Atom Count: 7,374
Modelled Residue Count: 783
Deposited Residue Count: 786
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A, B, C, D, E A, B, C, D, E, F	131	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C]	H [auth A], L [auth B], O [auth C]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain O [auth C] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain O [auth C]
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C]	K [auth B], M [auth C], N [auth C]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain R [auth E] MOL2 format, chain I [auth A] MOL2 format, chain R [auth E]	I [auth A], R [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain R [auth E] Interactions & Density Focus chain I [auth A] Focus chain R [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth A] SDF format, chain P [auth E] SDF format, chain Q [auth E] SDF format, chain S [auth F] SDF format, chain T [auth F] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth F] MOL2 format, chain T [auth F]	G [auth A] J [auth A] P [auth E] Q [auth E] S [auth F] G [auth A], J [auth A], P [auth E], Q [auth E], S [auth F], T [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain J [auth A] Focus chain P [auth E] Focus chain Q [auth E] Focus chain S [auth F] Focus chain T [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth A] Focus chain P [auth E] Focus chain Q [auth E] Focus chain S [auth F] Focus chain T [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.32 Å
R-Value Free: 0.191
R-Value Work: 0.145
R-Value Observed: 0.147
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M37THH

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.173	α = 90
b = 113.693	β = 93.02
c = 109.688	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-01-19

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History (Full details and data files)

Version 1.0: 2022-01-19
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

7THH

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)