9IZB | pdb_00009izb

Crystal structure of SARS-CoV-2 main protease in complex with TMP1

• PDB DOI: https://doi.org/10.2210/pdb9IZB/pdb

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


• Deposited: 2024-08-01 Released: 2025-05-28 
• Deposition Author(s): Deng, X.Y., Zeng, R., Yang, S.Y., Lei, J.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.253 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of SARS-CoV-2 main protease in complex with TMP1

Deng, X.Y., Zeng, R., Yang, S.Y., Lei, J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.54 kDa 
• Atom Count: 2,458 
• Modeled Residue Count: 306 
• Deposited Residue Count: 311 
• 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
TMP1	B	5	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FP9	B	L-PEPTIDE LINKING	C5 H8 F N O2		PRO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.253 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.162	α = 90
b = 53.71	β = 101.26
c = 44.258	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-28 
Deposition Author(s): Deng, X.Y., Zeng, R., Yang, S.Y., Lei, J.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2022YFC2303700

Revision History  

• Version 1.0: 2025-05-28
  Type: Initial release