7VVP | pdb_00007vvp

Crystal structure of SARS-Cov-2 main protease in complex with PF07304814

• PDB DOI: https://doi.org/10.2210/pdb7VVP/pdb

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


• Deposited: 2021-11-07 Released: 2022-08-24 
• Deposition Author(s): Zhou, X.L., Zhong, F.L., Lin, C., Zeng, P., Zhang, J., Li, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Structural Basis of Main Proteases of Coronavirus Bound to Drug Candidate PF-07304814

Li, J., Lin, C., Zhou, X., Zhong, F., Zeng, P., McCormick, P.J., Jiang, H., Zhang, J.

(2022) J Mol Biology 434: 167706

• DOI: https://doi.org/10.1016/j.jmb.2022.167706

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: 66.21 kDa 
• Atom Count: 4,739 
• Modeled Residue Count: 592 
• Deposited Residue Count: 592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	296	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
80I (Subject of Investigation/LOI)	C [auth B]	[(3~{S})-3-[[(2~{S})-2-[(4-methoxy-1~{H}-indol-2-yl)carbonylamino]-4-methyl-pentanoyl]amino]-2-oxidanylidene-4-[(3~{R})-2-oxidanylidene-3,4-dihydropyrrol-3-yl]butyl] dihydrogen phosphate C24 H33 N4 O9 P FQKALOFOWPDTED-WBAXXEDZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.074	α = 90
b = 102.273	β = 90
c = 103.746	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-24 
Deposition Author(s): Zhou, X.L., Zhong, F.L., Lin, C., Zeng, P., Zhang, J., Li, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-08-24
  Type: Initial release
  
• Version 2.0: 2023-05-31
  Type: Coordinate replacement
  Reason: Model orientation/position
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2023-11-29
  Changes: Data collection, Refinement description