2YNB | pdb_00002ynb

Crystal structure of the main protease of coronavirus HKU4 in complex with a Michael acceptor SG85

• PDB DOI: https://doi.org/10.2210/pdb2YNB/pdb

• Classification: HYDROLASE
• Organism(s): Tylonycteris bat coronavirus HKU4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-10-13 Released: 2013-10-23 
• Deposition Author(s): Ma, Q., Xiao, Y., Hilgenfeld, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.198 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Literature

Inhibitor for the Main Protease of Coronavirus Hku4

Ma, Q., Xiao, Y., 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)

Macromolecule Content 

• Total Structure Weight: 67.21 kDa 
• Atom Count: 5,190 
• Modeled Residue Count: 608 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-LIKE PROTEINASE	A, B	306	Tylonycteris bat coronavirus HKU4	Mutation(s): 0  EC: 3.4.22.69
UniProt
Find proteins for P0C6T4 (Bat coronavirus HKU4) Explore P0C6T4  Go to UniProtKB:  P0C6T4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G85	E [auth B]	N-[(benzyloxy)carbonyl]-O-tert-butyl-L-seryl-N-{(2R)-5-ethoxy-5-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]pentan-2-yl}-L-phenylalaninamide C35 H48 N4 O8 JRBUWNJDFCUWEM-CRNKYVSFSA-N
NI	C [auth A], D [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.198 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.35	α = 90
b = 79.35	β = 90
c = 178.67	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
XDS	data reduction
autoPROC	data scaling
XDS	data scaling
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-23 
Deposition Author(s): Ma, Q., Xiao, Y., Hilgenfeld, R.

Revision History  

• Version 1.0: 2013-10-23
  Type: Initial release
  
• Version 1.1: 2019-03-06
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.2: 2019-05-15
  Changes: Data collection, Experimental preparation
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary