8BFO

Structure of the apo form of Mpro from SARS-CoV-2

PDB DOI: https://doi.org/10.2210/pdb8BFO/pdb

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

Deposited: 2022-10-26 Released: 2023-11-08
Deposition Author(s): Medrano, F.J., Romero, A.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.286
R-Value Work: 0.212

wwPDB Validation 3D Report Full Report

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

Literature

Peptidyl Nitroalkenes Inhibit SARS-CoV-2 Main Protease and Block Virus Replication

Medrano, F.J., Romero, A.

To be published.

Macromolecule Content

Total Structure Weight: 33.7 kDa
Atom Count: 2,418
Modelled Residue Count: 305
Deposited Residue Count: 305
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	305	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.4.22.69
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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.286
R-Value Work: 0.212
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.98	α = 90
b = 53.933	β = 101.004
c = 44.738	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-11-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	Spain	PIE-202020E224

Revision History (Full details and data files)

Version 1.0: 2023-11-08
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.