7LW2 | pdb_00007lw2

Crystal structure of EV-D68 2A protease N84T mutant

• PDB DOI: https://doi.org/10.2210/pdb7LW2/pdb

• Classification: HYDROLASE
• Organism(s): enterovirus D68
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-02-27 Released: 2022-08-31 
• Deposition Author(s): Liu, C., Lee, M.-Y., Liu, W., Wang, J.
• 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: 2.57 Å
• R-Value Free: 
  0.242 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of EV-D68 2A protease C107A mutant

Liu, C., Lee, M.-Y., Ma, C., Liu, W., Wang, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 6 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 96.6 kDa 
• Atom Count: 6,169 
• Modeled Residue Count: 851 
• Deposited Residue Count: 882 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease 2A	A [auth E], B [auth A], C [auth B], D [auth C], E [auth D], F	147	enterovirus D68	Mutation(s): 1  EC: 3.4.22.29
UniProt
Find proteins for A0A097BW19 (Human enterovirus D68) Explore A0A097BW19  Go to UniProtKB:  A0A097BW19

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth E], H [auth A], I [auth B], J [auth C], K [auth D], L [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free:  0.242 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.255	α = 90
b = 119.255	β = 90
c = 80.326	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-31 
Deposition Author(s): Liu, C., Lee, M.-Y., Liu, W., Wang, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	NIH-NIAID-R01AI147325

Revision History  

• Version 1.0: 2022-08-31
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description