8FWN | pdb_00008fwn

Crystal structure of SARS-CoV-2 papain-like protease C111S mutant

PDB DOI: https://doi.org/10.2210/pdb8FWN/pdb

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

Deposited: 2023-01-23 Released: 2023-05-17
Deposition Author(s): Bezerra, E.H.S., Soprano, A.S., Tonoli, C.C.C., Prado, P.F.V., da Silva, J.C., Franchini, K.G., Trivella, D.B.B., Benedetti, C.E.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.198 (Depositor), 0.201 (DCC)
R-Value Work:
0.182 (Depositor), 0.185 (DCC)
R-Value Observed:
0.182 (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

Crystal structure of SARS-CoV-2 papain-like protease C111S mutant

Bezerra, E.H.S., Soprano, A.S., Tonoli, C.C.C., Prado, P.F.V., da Silva, J.C., Franchini, K.G., Trivella, D.B.B., Benedetti, C.E.

To be published.

Macromolecule Content

Total Structure Weight: 37.67 kDa
Atom Count: 3,020
Modeled Residue Count: 311
Deposited Residue Count: 324
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A	324	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain B [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain B [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain B [auth A]	B [auth A], E [auth A], F [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain B [auth A] Focus chain E [auth A] Focus chain F [auth A]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], H [auth A], I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth A] Focus chain I [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
ACT (Subject of Investigation/LOI) Query on ACT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]