7NXH

Structure of SARS-CoV2 NSP5 (3C-like proteinase) determined in-house

• PDB DOI: https://doi.org/10.2210/pdb7NXH/pdb

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


• Deposited: 2021-03-18 Released: 2022-01-26 
• Deposition Author(s): Calderone, V., Grifagni, D., Cantini, F., Fragai, M., Banci, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.268 
• R-Value Work: 0.216 
• R-Value Observed: 0.219 

Starting Model: experimental

Literature

SARS-CoV-2 M pro inhibition by a zinc ion: structural features and hints for drug design.

Grifagni, D., Calderone, V., Giuntini, S., Cantini, F., Fragai, M., Banci, L.

(2021) Chem Commun (Camb) 57: 7910-7913

• PubMed: 34278402 
• DOI: https://doi.org/10.1039/d1cc02956h
• Primary Citation of Related Structures:  
  7NWX, 7NXH


• PubMed Abstract: 
  

  Structural data on the SARS-CoV-2 main protease in complex with a zinc-containing organic inhibitor are already present in the literature and gave hints on the presence of a zinc binding site involving the catalytically relevant cysteine and histidine residues. In this paper, the structural basis of ionic zinc binding to the SARS-CoV-2 main protease has been elucidated by X-ray crystallography. The zinc binding affinity and its ability to inhibit the SARS-CoV-2 main protease have been investigated. These findings provide solid ground for the design of potent and selective metal-conjugated inhibitors of the SARS-CoV-2 main protease.

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Organizational Affiliation: 

Magnetic Resonance Center (CERM), University of Florence, via Sacconi 6, Sesto Fiorentino, 50019, Italy. [e-mail] [e-mail] [e-mail].

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: homology

Macromolecule Content

• Total Structure Weight: 33.83 kDa 
• Atom Count: 2,427 
• Modelled Residue Count: 306 
• 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  EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.268 
• R-Value Work: 0.216 
• R-Value Observed: 0.219 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.91	α = 90
b = 53.43	β = 101.85
c = 44.97	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-01-26 
Deposition Author(s): Calderone, V., Grifagni, D., Cantini, F., Fragai, M., Banci, L.

Revision History  

• Version 1.0: 2022-01-26
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description