7NBR | pdb_00007nbr

Crystal structure of SARS-CoV-2 main protease (Mpro) in complex with the HCV NS3/4A inhibitor boceprevir

• PDB DOI: https://doi.org/10.2210/pdb7NBR/pdb

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


• Deposited: 2021-01-27 Released: 2021-03-03 
• Deposition Author(s): Zhang, L., Hilgenfeld, R.
• Funding Organization(s): European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.269 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.184 (DCC) 

Starting Model: experimental

Literature

Crystal structure of SARS-CoV-2 main protease (Mpro) in complex with the HCV NS3/4A inhibitor boceprevir

Zhang, L., Hilgenfeld, R.

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: 34.38 kDa 
• Atom Count: 2,405 
• Modeled Residue Count: 302 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A [auth AAA]	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U5G (Subject of Investigation/LOI)	B [auth AAA]	boceprevir (bound form) C27 H47 N5 O5 FEBWCINGHXXUCV-GFLQDLJJSA-N
CL	C [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 

1 Unique

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.269 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.184 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.767	α = 90
b = 53.37	β = 101.833
c = 45.949	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
SCALA	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-03-03 
Deposition Author(s): Zhang, L., Hilgenfeld, R.

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Funding Organization	Location	Grant Number
European Commission	European Union	SCORE

Revision History  

• Version 1.0: 2021-03-03
  Type: Initial release
  
• Version 1.1: 2021-04-21
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Refinement description
• Version 1.2: 2021-04-28
  Changes: Source and taxonomy, Structure summary
• Version 1.3: 2024-01-31
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary