7GPX

PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3C Protease in complex with NCL-00024661

• PDB DOI: https://doi.org/10.2210/pdb7GPX/pdb
• Deposition Group: G_1002271 (changed state) ExploreG_1002271

• Classification: VIRAL PROTEIN
• Organism(s): enterovirus D68
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-08-24 Released: 2023-11-29 
• Deposition Author(s): Lithgo, R.M., Fairhead, M., Koekemoer, L., Aschenbrenner, J.C., Balcomb, B.H., Godoy, A.S., Marples, P.G., Ni, X., Tomlinson, C.W.E., Thompson, W., Wild, C., Fearon, D., Walsh, M.A., von Delft, F.
• 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: 1.20 Å
• R-Value Free: 0.188 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 

Literature

PanDDA analysis group deposition

Lithgo, R.M., Fairhead, M., Koekemoer, L., Aschenbrenner, J.C., Balcomb, B.H., Godoy, A.S., Marples, P.G., Ni, X., Tomlinson, C.W.E., Thompson, W., Wild, C., Fearon, D., Walsh, M.A., von Delft, F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.92 kDa 
• Atom Count: 3,258 
• Modelled Residue Count: 361 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease 3C	A, B	182	enterovirus D68	Mutation(s): 0  EC: 3.4.22.28
UniProt
Find proteins for Q68T42 (Human enterovirus D68) Explore Q68T42  Go to UniProtKB:  Q68T42

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UUJ (Subject of Investigation/LOI)	D [auth B]	5-bromo-2-hydroxybenzonitrile C7 H4 Br N O PVCONXMDUZOPJH-UHFFFAOYSA-N
DMS	C [auth A], E [auth B], F [auth B], G [auth B], H [auth B], I [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.188 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.997	α = 90
b = 61.244	β = 90
c = 147.79	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-29 
Deposition Author(s): Lithgo, R.M., Fairhead, M., Koekemoer, L., Aschenbrenner, J.C., Balcomb, B.H., Godoy, A.S., Marples, P.G., Ni, X., Tomlinson, C.W.E., Thompson, W., Wild, C., Fearon, D., Walsh, M.A., von Delft, F.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1U19AI171399

Revision History  

• Version 1.0: 2023-11-29
  Type: Initial release