7SQE | pdb_00007sqe

Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with Jun9-84-3 inhibitor

PDB DOI: https://doi.org/10.2210/pdb7SQE/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-11-05 Released: 2021-11-17
Deposition Author(s): Osipiuk, J., Tesar, C., Endres, M., Wang, J., 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: 2.00 Å
R-Value Free:
0.205 (Depositor)
R-Value Work:
0.174 (Depositor)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with Jun9-84-3 inhibitor

Osipiuk, J., Tesar, C., Endres, M., Wang, J., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 109.45 kDa
Atom Count: 8,068
Modeled Residue Count: 941
Deposited Residue Count: 954
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease	A, B, C	318	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1 EC: 3.4.19.12
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JWX (Subject of Investigation/LOI) Query on JWX Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] SDF format, chain P [auth C] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain P [auth C] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain P [auth C]	D [auth A], I [auth B], P [auth C]	(1R)-N-[(1H-indol-3-yl)methyl]-N-methyl-1-(naphthalen-1-yl)ethan-1-amine C₂₂ H₂₂ N₂ SKQKRKDBQBKZJK-MRXNPFEDSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain P [auth C] Interactions & Density Focus chain D [auth A] Focus chain I [auth B] Focus chain P [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain Q [auth C] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain Q [auth C] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain Q [auth C]	E [auth A], J [auth B], Q [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain Q [auth C] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain Q [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain T [auth C] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain T [auth C]	H [auth A], L [auth B], M [auth B], N [auth B], T [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain T [auth C] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain T [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C]	F [auth A] G [auth A] K [auth B] O [auth B] R [auth C] F [auth A], G [auth A], K [auth B], O [auth B], R [auth C], S [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C]