8W3T

Crystal Structure of Enterovirus 68 3C Protease with GC376 at 1.98 Angstroms

PDB DOI: https://doi.org/10.2210/pdb8W3T/pdb

Classification: VIRAL PROTEIN,HYDROLASE/INHIBITOR
Organism(s): enterovirus D68
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2024-02-22 Released: 2025-01-15
Deposition Author(s): Azzolino, V.N., Shaqra, A.M., Schiffer, C.A.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.234
R-Value Work: 0.199
R-Value Observed: 0.200

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural Analysis of Inhibitor Binding to Enterovirus-D68 3C Protease

Azzolino, V.N., Shaqra, A.M., Ali, A., Yilmaz, N.K., Schiffer, C.A.

(2025) Viruses

DOI: https://doi.org/10.3390/v17010075

Macromolecule Content

Total Structure Weight: 21.51 kDa
Atom Count: 1,632
Modelled Residue Count: 188
Deposited Residue Count: 190
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A	190	enterovirus D68	Mutation(s): 0 EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for A1E4A3 (Human enterovirus D68) Explore A1E4A3 Go to UniProtKB: A1E4A3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1E4A3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UED (Subject of Investigation/LOI) Query on UED Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide C₂₁ H₃₁ N₃ O₅ JUCVXDDMQHPCKT-BZSNNMDCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.234
R-Value Work: 0.199
R-Value Observed: 0.200
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.174	α = 90
b = 56.174	β = 90
c = 170.629	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
Coot	model building
XDS	data reduction
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1F30AI181515-01

Revision History (Full details and data files)

Version 1.0: 2025-01-15
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.