7GPZ | pdb_00007gpz

PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3C Protease in complex with NCL-00024673


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 
    0.228 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.192 (Depositor) 
  • R-Value Observed: 
    0.193 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Crystallographic Fragment Screen of Coxsackievirus A16 2A Protease identifies new opportunities for the development of broad-spectrum anti-enterovirals.

Lithgo, R.M.Tomlinson, C.W.E.Fairhead, M.Winokan, M.Thompson, W.Wild, C.Aschenbrenner, J.C.Balcomb, B.H.Marples, P.G.Chandran, A.V.Golding, M.Koekemoer, L.Williams, E.P.Wang, S.Ni, X.MacLean, E.Giroud, C.Godoy, A.S.Xavier, M.A.Walsh, M.Fearon, D.von Delft, F.

(2024) bioRxiv 

Macromolecule Content 

  • Total Structure Weight: 40.46 kDa 
  • Atom Count: 3,147 
  • Modeled Residue Count: 362 
  • Deposited Residue Count: 364 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protease 3C
A, B
182enterovirus D68Mutation(s): 0 
EC: 3.4.22.28
UniProt
Find proteins for Q68T42 (Human enterovirus D68)
Explore Q68T42 
Go to UniProtKB:  Q68T42
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ68T42
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UUV
(Subject of Investigation/LOI)

Query on UUV



Download:Ideal Coordinates CCD File
C [auth B]4-bromo-1-(2-methoxyethyl)-1H-pyrazole
C6 H9 Br N2 O
SJIMZWZHTDHXRI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free:  0.228 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.192 (Depositor) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.73α = 90
b = 62.348β = 90
c = 147.775γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU19AI171399

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-29
    Type: Initial release
  • Version 1.1: 2024-09-11
    Changes: Author supporting evidence
  • Version 1.2: 2024-10-16
    Changes: Database references, Structure summary