8U3O | pdb_00008u3o

SARS-CoV-2 Main Protease A173V in complex with CDD-1819

• PDB DOI: https://doi.org/10.2210/pdb8U3O/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2023-09-08 Released: 2024-09-18 
• Deposition Author(s): Nnabuife, C., Palzkill, T.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.235 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

SARS-CoV-2 Main Protease A173V in complex with CDD-1819

Nnabuife, C., Palzkill, T.

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)

Macromolecule Content 

• Total Structure Weight: 68.93 kDa 
• Atom Count: 5,146 
• Modeled Residue Count: 595 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF1a polyprotein	A, B	307	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  Gene Names: ORF1ab
UniProt
Find proteins for A0A7U3H5H9 (Severe acute respiratory syndrome coronavirus 2) Explore A0A7U3H5H9  Go to UniProtKB:  A0A7U3H5H9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O69 (Subject of Investigation/LOI)	C [auth A], D [auth B]	(2P)-2-(isoquinolin-4-yl)-1-[(1s,3R)-3-(methylcarbamoyl)cyclobutyl]-N-[(1S)-1-(naphthalen-2-yl)ethyl]-1H-benzimidazole-7-carboxamide C35 H31 N5 O2 YXZCMQAWBHCPMS-NJTBCWBZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.235 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.057	α = 90
b = 101.129	β = 90
c = 105.293	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: 2024-09-18 
Deposition Author(s): Nnabuife, C., Palzkill, T.

---

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

Revision History  

• Version 1.0: 2024-09-18
  Type: Initial release