5NFS

Structure of coxsackievirus B3 3C protease in complex with the alpha-ketoamide (S)-N-benzyl-3-((S)-2-cinnamamido-3-phenylpropanamido)-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butanamide (cinnamoyl-phenylalanine-GlnLactam-CO-CO-NH-benzyl)

PDB DOI: https://doi.org/10.2210/pdb5NFS/pdb

Classification: VIRAL PROTEIN
Organism(s): Coxsackievirus B3
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-03-15 Released: 2018-05-16
Deposition Author(s): Ma, Q., Zhang, L., Hilgenfeld, R.
Funding Organization(s): German Center for Infection Research (DZIF)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.239 (Depositor), 0.250 (DCC)
R-Value Work:
0.179 (Depositor), 0.190 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Alpha-ketoamides as broad-spectrum inhibitors of coronavirus and enterovirus replication

Lin, D., Zhang, L., Kusov, Y., Nian, Y., Ma, Q., Wang, J., Leyssen, P., Lanko, K., Neyts, J., de Wilde, A., Snijder, E.J., Liu, H., Hilgenfeld, R.

To be published.

Macromolecule Content

Total Structure Weight: 21 kDa
Atom Count: 1,546
Modelled Residue Count: 180
Deposited Residue Count: 184
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	184	Coxsackievirus B3	Mutation(s): 0
UniProt
Find proteins for Q5UEA2 (Coxsackievirus B3) Explore Q5UEA2 Go to UniProtKB: Q5UEA2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5UEA2
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D03 Query on D03 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]	(S)-N-benzyl-3-((S)-2-cinnamamido-3-phenylpropanamido)-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butanamide C₃₃ H₃₆ N₄ O₅ ZTFAWEJBUOCZIL-NHTHZNHESA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.239 (Depositor), 0.250 (DCC)
R-Value Work: 0.179 (Depositor), 0.190 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.657	α = 90
b = 64.354	β = 115.44
c = 39.477	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-05-16

Deposition Author(s):

Funding Organization	Location	Grant Number
German Center for Infection Research (DZIF)	Germany	TTU 01.803

Revision History (Full details and data files)

Version 1.0: 2018-05-16
Type: Initial release
Version 1.1: 2024-05-01
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary

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.