7CX9 | pdb_00007cx9

Crystal structure of the SARS-CoV-2 main protease in complex with INZ-1

• PDB DOI: https://doi.org/10.2210/pdb7CX9/pdb

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


• Deposited: 2020-09-01 Released: 2020-09-16 
• Deposition Author(s): Zeng, R., Liu, X.L., Qiao, J.X., Nan, J.S., Wang, Y.F., Li, Y.S., Yang, S.Y., Lei, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.180 (DCC) 

Starting Model: experimental

Literature

Crystal structure of the SARS-CoV-2 main protease in complex with INZ-1

Qiao, J.X., Zeng, R., Liu, X.L., Nan, J.S., Wang, Y.F., Li, Y.S., Lei, J., Yang, S.Y.

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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.23 kDa 
• Atom Count: 2,696 
• Modeled Residue Count: 295 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GKF (Subject of Investigation/LOI)	B [auth A]	3-iodanyl-1~{H}-indazole-7-carbaldehyde C8 H5 I N2 O QWWAONJINWEHJL-UHFFFAOYSA-N
GOL (Subject of Investigation/LOI)	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.180 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.236	α = 90
b = 82.9	β = 115.123
c = 51.489	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-16 
Deposition Author(s): Zeng, R., Liu, X.L., Qiao, J.X., Nan, J.S., Wang, Y.F., Li, Y.S., Yang, S.Y., Lei, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	2020YFS0010/HX2019nCoV039

Revision History  

• Version 1.0: 2020-09-16
  Type: Initial release
  
• Version 1.1: 2021-03-10
  Changes: Structure summary
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary