8R26

SARS-CoV-2 Mpro (Omicron,P132H) in complex with alpha-ketoamide 13b-K at pH 8.5

PDB DOI: https://doi.org/10.2210/pdb8R26/pdb

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

Deposited: 2023-11-03 Released: 2024-11-13
Deposition Author(s): Ibrahim, M., Sun, X., Hilgenfeld, R.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 ?
R-Value Free: 0.245
R-Value Work: 0.192
R-Value Observed: 0.195

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

SARS-CoV-2 Mpro (Omicron,P132H) in complex with alpha-ketoamide 13b-K at pH 8.5

Ibrahim, M., Hilgenfeld, R., Sun, X.

To be published.

Macromolecule Content

Total Structure Weight: 137.96 kDa
Atom Count: 10,002
Modelled Residue Count: 1,220
Deposited Residue Count: 1,224
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, B, C [auth D], D [auth C]	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1 EC: 3.4.22.69
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1 Go to UniProtKB: P0DTC1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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 E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth D] SDF format, chain J [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth D] MOL2 format, chain J [auth C] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth D] mmCIF format, chain J [auth C]	E [auth A], G [auth B], H [auth D], J [auth C]	~{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 A] Focus chain G [auth B] Focus chain H [auth D] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth D] Focus chain J [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth D] SDF format, chain K [auth C] MOL2 format, chain F [auth A] MOL2 format, chain I [auth D] MOL2 format, chain K [auth C] mmCIF format, chain F [auth A] mmCIF format, chain I [auth D] mmCIF format, chain K [auth C]	F [auth A], I [auth D], K [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain I [auth D] Focus chain K [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth D] Focus chain K [auth C]