7TOB | pdb_00007tob

Crystal structure of the SARS-CoV-2 Omicron main protease (Mpro) in complex with inhibitor GC376

PDB DOI: https://doi.org/10.2210/pdb7TOB/pdb

Classification: VIRAL PROTEIN/INHIBITOR
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2022-01-24 Released: 2022-02-02
Deposition Author(s): Sacco, M.D., Wang, J., Chen, Y.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.213 (Depositor), 0.217 (DCC)
R-Value Work:
0.172 (Depositor), 0.179 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

The P132H mutation in the main protease of Omicron SARS-CoV-2 decreases thermal stability without compromising catalysis or small-molecule drug inhibition.

Sacco, M.D., Hu, Y., Gongora, M.V., Meilleur, F., Kemp, M.T., Zhang, X., Wang, J., Chen, Y.

(2022) Cell Res 32: 498-500

PubMed: 35292745 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41422-022-00640-y
Primary Citation Related Structures:
7TOB

Organizational Affiliation

Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.

Macromolecule Content

Total Structure Weight: 34.56 kDa
Atom Count: 2,613
Modeled Residue Count: 306
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

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| 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): 1 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K36 (Subject of Investigation/LOI) Query on K36 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]	(1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid C₂₁ H₃₁ N₃ O₈ S BSPZFJDYQHDZNR-HTCLRFROSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002495 (K36) Query on PRD_002495	B [auth A]	GC376	Peptide-like / Inhibitor		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.213 (Depositor), 0.217 (DCC)
R-Value Work: 0.172 (Depositor), 0.179 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.186	α = 90
b = 52.987	β = 100.5
c = 113.006	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-02-02

Deposition Author(s):

Sacco, M.D.

Wang, J.

Chen, Y.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI158775
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI147325
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI157046