Macromolecule Content

Total Structure Weight: 70.00 kDa
Atom Count: 5231
Modelled Residue Count: 625
Deposited Residue Count: 632
Unique protein chains: 2

7T9Y

Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 8/9

PDB DOI: 10.2210/pdb7T9Y/pdb

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

Deposited: 2021-12-20 Released: 2022-06-22
Deposition Author(s): Shaqra, A.M., Schiffer, C.A.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.236
R-Value Work: 0.179
R-Value Observed: 0.182

wwPDB Validation 3D Report Full Report

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

Literature

Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 8/9

Shaqra, A.M., Schiffer, C.A.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1 Gene Names: rep, 1a-1b EC: 3.4.22.69 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
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
Protein Feature View Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nonstructural protein 8/9	C, D	10	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B]	E [auth A], F [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.236
R-Value Work: 0.179
R-Value Observed: 0.182
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.229	α = 90
b = 98.87	β = 90
c = 101.62	γ = 90

Software Package:

Software Name	Purpose
CrysalisPro	data scaling
PHENIX	refinement
CrysalisPro	data reduction
Coot	model building
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Deposited Date: 2021-12-20
Released Date: 2022-06-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	United States	--

Revision History (Full details and data files)

Version 1.0: 2022-06-22
Type: Initial release

RCSB PDB is 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.