7PFM | pdb_00007pfm

A SARS-CoV2 major protease non-covalent ligand structure determined to 2.0 A resolution

PDB DOI: https://doi.org/10.2210/pdb7PFM/pdb

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

Deposited: 2021-08-11 Released: 2022-08-24
Deposition Author(s): Moche, M., Moodie, L., Strandback, E., Nyman, T., Sandstrom, A., Akaberi, D., Lennerstrand, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.220 (Depositor), 0.222 (DCC)
R-Value Work:
0.181 (Depositor), 0.183 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7PFM

Ligand Structure Quality Assessment

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

Literature

The SARS-CoV2 major protease (Mpro) in complex with a non-covalent inhibitory ligand at 2 A resolution

Moche, M., Moodie, L., Strandback, E., Nyman, T., Akaberi, D., Lennerstrand, J.

To be published.

Macromolecule Content

Total Structure Weight: 68.52 kDa
Atom Count: 5,082
Modeled Residue Count: 610
Deposited Residue Count: 612
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1ab	A, B	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7IL (Subject of Investigation/LOI) Query on 7IL Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	N-[(1R)-2-(tert-butylamino)-2-oxidanylidene-1-pyridin-3-yl-ethyl]-N-(4-tert-butylphenyl)-1H-imidazole-5-carboxamide C₂₅ H₃₁ N₅ O₂ AJXIAISTEXNTHM-OAQYLSRUSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.220 (Depositor), 0.222 (DCC)
R-Value Work: 0.181 (Depositor), 0.183 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.233	α = 90
b = 53.947	β = 99.77
c = 115.038	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-24

Deposition Author(s):

Lennerstrand, J.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-08-24
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.