9J8T | pdb_00009j8t

Crystal structure of SARS-CoV-2 main protease in complex with Mp-4L2

• PDB DOI: https://doi.org/10.2210/pdb9J8T/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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.265 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

De novo discovery of a non-covalent cell-penetrating bicyclic peptide 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: surface plasmon resonance

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.78 kDa 
• Atom Count: 2,578 
• Modeled Residue Count: 316 
• Deposited Residue Count: 322 
• Unique protein chains: 2

Macromolecules

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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TYR-DSG-DLE-DPN-DGN-ARG-DTH-DAS-DTR-DTH-ALO-DGN-DTY-CCJ-GLY-NH2	B [auth C]	16	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  2 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
ALO	B [auth C]	THR	Stereoisomerisation	C4 H9 N O3
CCJ	B [auth C]	DCY	Carboxymethylation	C5 H9 N O4 S

Non-standard Monomers  8 Unique
ID	Chains	Type	Formula	2D Diagram
DAS	B [auth C]	D-PEPTIDE LINKING	C4 H7 N O4
DGN	B [auth C]	D-PEPTIDE LINKING	C5 H10 N2 O3
DLE	B [auth C]	D-PEPTIDE LINKING	C6 H13 N O2
DPN	B [auth C]	D-PEPTIDE LINKING	C9 H11 N O2
DSG	B [auth C]	D-PEPTIDE LINKING	C4 H8 N2 O3
DTH	B [auth C]	D-PEPTIDE LINKING	C4 H9 N O3
DTR	B [auth C]	D-PEPTIDE LINKING	C11 H12 N2 O2
DTY	B [auth C]	D-PEPTIDE LINKING	C9 H11 N O3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.265 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.848	α = 90
b = 80.659	β = 114.54
c = 51.502	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Shi, Y.S., Yang, J.Y., Wang, M.W.

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

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release