7CUT | pdb_00007cut

Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with Z-VAD-FMK

• PDB DOI: https://doi.org/10.2210/pdb7CUT/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-08-24 Released: 2021-06-23 
• Deposition Author(s): Lu, M., Yang, H.T., Wang, Z.Y., Zhao, Y., Xing, Y.F.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Other government

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.223 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Identification of proteasome and caspase inhibitors targeting SARS-CoV-2 M pro .

Wang, Z., Zhao, Y., Wang, Q., Xing, Y., Feng, L., Kong, J., Peng, C., Zhang, L., Yang, H., Lu, M.

(2021) Signal Transduct Target Ther 6: 214-214

• PubMed: 34075025 
• DOI: https://doi.org/10.1038/s41392-021-00639-8
• Primary Citation Related Structures: 
  7CUT, 7CUU

---

Organizational Affiliation: 
• Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.
National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, China.
State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China. [e-mail].
Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China. [e-mail].
Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 34.67 kDa 
• Atom Count: 2,562 
• Modeled Residue Count: 306 
• Deposited Residue Count: 311 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C protein	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Z-VAD(OMe)-FMK	B	5	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FL6	B	L-PEPTIDE LINKING	C5 H9 N O4		ASP

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002352	B	Z-VAD(OMe)-FMK	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.223 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.22	α = 90
b = 82.65	β = 115.28
c = 51.74	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-06-23 
Deposition Author(s): Lu, M., Yang, H.T., Wang, Z.Y., Zhao, Y., Xing, Y.F.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81520108019
National Natural Science Foundation of China (NSFC)	China	813300237
Other government	China	Clinical Research Program of Ruijin Hospital (2018CR006)
Other government	China	Shanghai Youth Talent Development Program (2017275)
Other government	China	Shanghai Medical and Health Excellent Discipline Leader Development Plan (2018BR36)
Other government	China	Shanghai Collaborative Innovation Center for Translational Medicine (TM201902)
Other government	China	Foundation of National Facility for Translational Medicine (Shanghai) (TMSK-2020-003)

Revision History  

• Version 1.0: 2021-06-23
  Type: Initial release
  
• Version 1.1: 2021-07-07
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Derived calculations, Refinement description