7GOP

PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3C Protease in complex with Z2033637875

PDB DOI: https://doi.org/10.2210/pdb7GOP/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.219
R-Value Work: 0.184
R-Value Observed: 0.185

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 40.46 kDa
Atom Count: 3,189
Modelled Residue Count: 362
Deposited Residue Count: 364
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q68T42
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LRF (Subject of Investigation/LOI) Query on LRF Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B]	C [auth B]	N~2~-(4-cyano-3-methyl-1,2-thiazol-5-yl)-N~2~-methylglycinamide C₈ H₁₀ N₄ O S BCFQGXBWVPWHCV-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.219
R-Value Work: 0.184
R-Value Observed: 0.185
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.05	α = 90
b = 61.64	β = 90
c = 147.8	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-11-29

Deposition Author(s):

Aschenbrenner, J.C.

Tomlinson, C.W.E.

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

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.