9J8U | pdb_00009j8u

Crystal structure of SARS-CoV-2 main protease in complex with Mp-4D7

PDB DOI: https://doi.org/10.2210/pdb9J8U/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2, synthetic construct
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-08-21 Released: 2025-07-02
Deposition Author(s): Shi, Y.S., Yang, J.Y., Wang, M.W.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free:
0.245 (Depositor), 0.245 (DCC)
R-Value Work:
0.204 (Depositor), 0.204 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

De novo discovery of a non-covalent cell-penetrating bicyclic pep-tide inhibitor targeting SARS-CoV-2 main protease

Yin, Y.Y., Shi, Y.S., Qi, J.Q., Tan, Y.T., Yang, J.Y., Wang, M.W., Peng, Q.P., Li, Y.L., Fu, L.F., Zhang, M.Z., Zhang, Y.Z.

To be published.

Macromolecule Content

Total Structure Weight: 35.56 kDa
Atom Count: 2,472
Modeled Residue Count: 316
Deposited Residue Count: 322
Unique protein chains: 2

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	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DTY-VAL-THR-PHE-HIS-ALO-2TL-2TL-PRO-PHE-LEU-DPR-PRO-CCJ-GLY-NH2	B [auth C]	16	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALO Query on ALO	B [auth C]	L-PEPTIDE LINKING	C₄ H₉ N O₃		THR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free: 0.245 (Depositor), 0.245 (DCC)
R-Value Work: 0.204 (Depositor), 0.204 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.26	α = 90
b = 78.26	β = 90
c = 294.272	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	refinement
autoPROC	data processing
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-02

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2025-07-02
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.