6WNP | pdb_00006wnp

X-ray Structure of SARS-CoV-2 main protease bound to Boceprevir at 1.45 A

• PDB DOI: https://doi.org/10.2210/pdb6WNP/pdb

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


• Deposited: 2020-04-23 Released: 2020-05-06 
• Deposition Author(s): Anson, B., Mesecar, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 
  0.196 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

X-ray Structure of SARS-CoV-2 main protease bound to Boceprevir at 1.45 A

Anson, B., Mesecar, A.

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: 34.35 kDa 
• Atom Count: 2,804 
• Modeled 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  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U5G	B [auth A]	boceprevir (bound form) C27 H47 N5 O5 FEBWCINGHXXUCV-GFLQDLJJSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002382 (U5G)	B [auth A]	Boceprevir (bound form)	Peptide-like / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free:  0.196 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.549	α = 90
b = 81.086	β = 116.979
c = 54.669	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-05-06 
Deposition Author(s): Anson, B., Mesecar, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2020-05-06
  Type: Initial release
  
• Version 1.1: 2020-05-13
  Changes: Derived calculations, Structure summary
• Version 1.2: 2020-06-10
  Changes: Structure summary
• Version 1.3: 2023-10-18
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary