8R0V | pdb_00008r0v

SARS-CoV-2 Mpro (Omicron, P132H) in complex with alpha-ketoamide 13b-K at pH 6.5

PDB DOI: https://doi.org/10.2210/pdb8R0V/pdb

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

Deposited: 2023-11-01 Released: 2023-11-29
Deposition Author(s): Ibrahim, M., Sun, X., Hilgenfeld, R.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free:
0.247 (Depositor), 0.250 (DCC)
R-Value Work:
0.210 (Depositor), 0.210 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Why is the Omicron main protease of SARS-CoV-2 less stable than its wild-type counterpart? A crystallographic, biophysical, and theoretical study

Ibrahim, M., Sun, X., Martins de Oliveira, V., Liu, R., Clayton, J., El Kilani, H., Shen, J., Hilgenfeld, R.

(2024) Hlife 2: 419-433

DOI: https://doi.org/10.1016/j.hlife.2024.06.003

Macromolecule Content

Total Structure Weight: 137.85 kDa
Atom Count: 9,757
Modeled Residue Count: 1,220
Deposited Residue Count: 1,224
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 [auth C], B, C [auth D], D [auth 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% 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
O6K (Subject of Investigation/LOI) Query on O6K Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth D] SDF format, chain F [auth B] SDF format, chain E [auth C] MOL2 format, chain H [auth A] MOL2 format, chain G [auth D] MOL2 format, chain F [auth B] MOL2 format, chain E [auth C] mmCIF format, chain H [auth A] mmCIF format, chain G [auth D] mmCIF format, chain F [auth B] mmCIF format, chain E [auth C]	E [auth C], F [auth B], G [auth D], H [auth A]	~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate C₃₁ H₄₁ N₅ O₇ FRACPXUHUTXLCX-BELIEFIBSA-N		Interactions Focus chain E [auth C] Focus chain F [auth B] Focus chain G [auth D] Focus chain H [auth A] Interactions & Density Focus chain E [auth C] Focus chain F [auth B] Focus chain G [auth D] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free: 0.247 (Depositor), 0.250 (DCC)
R-Value Work: 0.210 (Depositor), 0.210 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.853	α = 84.722
b = 71.803	β = 80.368
c = 85.725	γ = 78.391

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-11-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	Germany	--

Revision History (Full details and data files)

Version 1.0: 2023-11-29
Type: Initial release
Version 1.1: 2024-11-13
Changes: Structure summary
Version 1.2: 2025-04-09
Changes: Database references

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.