8Y7T

Crystal structure of SARS-CoV-2 main protease in complex with C2

PDB DOI: https://doi.org/10.2210/pdb8Y7T/pdb

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

Deposited: 2024-02-05 Released: 2025-02-05
Deposition Author(s): Zeng, R., Deng, X.Y., Yang, Z.Y., Wang, K., Jiang, Y.Y., Lei, J.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 ?
R-Value Free:
0.266 (Depositor), 0.265 (DCC)
R-Value Work:
0.201 (Depositor), 0.207 (DCC)
R-Value Observed:
0.204 (Depositor)

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

Crystal structure of SARS-CoV-2 main protease in complex with C2

Zeng, R., Deng, X.Y., Yang, Z.Y., Wang, K., Jiang, Y.Y., Lei, J.

To be published.

Macromolecule Content

Total Structure Weight: 34.26 kDa
Atom Count: 2,437
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): 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1LX1 (Subject of Investigation/LOI) Query on A1LX1 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]	6-(iminomethyl)-4-(2-pyridin-2-ylethyl)-2-[4-(trifluoromethyl)phenyl]-1,2,4-triazine-3,5-dione C₁₈ H₁₄ F₃ N₅ O₂ YEBJSFQNRVLLRG-JJFYIABZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 ?
R-Value Free: 0.266 (Depositor), 0.265 (DCC)
R-Value Work: 0.201 (Depositor), 0.207 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 113.08	α = 90
b = 53.97	β = 101.03
c = 45.07	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOLREP	phasing
Aimless	data scaling
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-02-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2022YFC2303701

Revision History (Full details and data files)

Version 1.0: 2025-02-05
Type: Initial release

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.