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

Starting Model: experimental
View more details

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)
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] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF 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 N [auth C] SDF format, chain K [auth B] SDF format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain M [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] mmCIF format, chain I [auth A] mmCIF 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 J [auth A] SDF format, chain Q [auth E] SDF format, chain G [auth A] SDF format, chain P [auth E] SDF format, chain S [auth F] SDF format, chain T [auth F] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth E] MOL2 format, chain G [auth A] MOL2 format, chain P [auth E] MOL2 format, chain S [auth F] MOL2 format, chain T [auth F] mmCIF format, chain J [auth A] mmCIF format, chain Q [auth E] mmCIF format, chain G [auth A] mmCIF format, chain P [auth E] mmCIF format, chain S [auth F] mmCIF 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