7MPB | pdb_00007mpb

SARS Coronavirus-2 Main Protease 3CL-pro binding Ascorbate

• PDB DOI: https://doi.org/10.2210/pdb7MPB/pdb

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


• Deposited: 2021-05-04 Released: 2021-05-12 
• Deposition Author(s): Pandey, S., Malla, T.N., Stojkovic, E.A., Schmidt, M.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.244 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Vitamin C inhibits SARS coronavirus-2 main protease essential for viral replication

Malla, T.N., Pandey, S., Poudyal, I., Aldama, L., Feliz, D., Noda, M., Phillips, G.N., Stojkovic, E.A., Schmidt, M.

(2021) bioRxiv 

• DOI: https://doi.org/10.1101/2021.05.02.442358

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)

Macromolecule Content 

• Total Structure Weight: 70.17 kDa 
• Atom Count: 4,972 
• Modeled Residue Count: 613 
• Deposited Residue Count: 628 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	314	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ASC (Subject of Investigation/LOI)	C [auth A], E [auth B]	ASCORBIC ACID C6 H8 O6 CIWBSHSKHKDKBQ-JLAZNSOCSA-N
ETF	D [auth A], F [auth B]	TRIFLUOROETHANOL C2 H3 F3 O RHQDFWAXVIIEBN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.244 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.35	α = 90
b = 67.46	β = 90
c = 157.509	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-05-12 
Deposition Author(s): Pandey, S., Malla, T.N., Stojkovic, E.A., Schmidt, M.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--

Revision History  

• Version 1.0: 2021-05-12
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description