7SH8

Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI88

PDB DOI: https://doi.org/10.2210/pdb7SH8/pdb

Classification: VIRAL PROTEIN,HYDROLASE/INHIBITOR
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-10-08 Released: 2023-04-12
Deposition Author(s): Yang, K.S., Liu, W.R.
Funding Organization(s): Welch Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.272
R-Value Work: 0.234
R-Value Observed: 0.236

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure of the SARS-CoV-2 main protease in complex with inhibitors

Yang, K.S., Sankaran, B., Liu, W.R.

To be published.

Macromolecule Content

Total Structure Weight: 34.49 kDa
Atom Count: 2,617
Modelled Residue Count: 301
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	306	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GJ3 (Subject of Investigation/LOI) Query on GJ3 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	benzyl [(2S,3R)-1-{[(2S)-1-(2-acetyl-2-{[(3S)-2-oxopyrrolidin-3-yl]methyl}hydrazinyl)-3-cyclohexyl-1-oxopropan-2-yl]amino}-3-tert-butoxy-1-oxobutan-2-yl]carbamate (non-preferred name) C₃₂ H₄₉ N₅ O₇ LQGMWKMFHKDJKF-FBZFJNBBSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.272
R-Value Work: 0.234
R-Value Observed: 0.236
Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.704	α = 90
b = 83.413	β = 96.7
c = 86.416	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-04-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Welch Foundation	United States	--

Revision History (Full details and data files)

Version 1.0: 2023-04-12
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection
Version 1.3: 2024-11-20
Changes: Structure summary

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.