8VEC

Deep Mutational Scanning of SARS-CoV-2 PLpro

PDB DOI: https://doi.org/10.2210/pdb8VEC/pdb

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

Deposited: 2023-12-18 Released: 2024-03-20
Deposition Author(s): Wu, X., Nguyen, J.V., Call, M.E., Call, M.J.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.217
R-Value Work: 0.174
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Mutational Profiling of SARS-CoV-2 PLpro in human cells reveals requirements for function, structure, and drug escape

Wu, X., Go, M., Nguyen, J.V., Kuchel, N.W., Lu, B.G.C., Lowes, K.N., Calleja, D.J., Mitchell, J.P., Lessene, G., Komander, D., Call, M.E., Call, M.J.

(2024) Biorxiv

DOI: https://doi.org/10.1101/2024.03.11.584210

Macromolecule Content

Total Structure Weight: 36.1 kDa
Atom Count: 2,750
Modelled Residue Count: 318
Deposited Residue Count: 318
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	318	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.217
R-Value Work: 0.174
R-Value Observed: 0.177
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.958	α = 90
b = 85.47	β = 90
c = 82.88	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHENIX	phasing
XDS	data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-03-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	222698/Z/21/Z

Revision History (Full details and data files)

Version 1.0: 2024-03-20
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.