3ZZD | pdb_00003zzd

Crystal structure of 3C protease mutant (T68A and N126Y) of coxsackievirus B3 complexed with alpha, beta-unsaturated ethyl ester inhibitor 85

PDB DOI: https://doi.org/10.2210/pdb3ZZD/pdb

Classification: HYDROLASE
Organism(s): Coxsackievirus B3
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2011-08-31 Released: 2012-09-19
Deposition Author(s): Tan, J., Anand, K., Mesters, J.R., Hilgenfeld, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.257 (Depositor), 0.258 (DCC)
R-Value Work:
0.195 (Depositor), 0.195 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Peptidic Alpha, Beta-Unsaturated Ethyl Esters as Inhibitors of the 3C Protease of Coxsackie Virus B3: Crystal Structures, Antiviral Activities, and Resistance Mutations

Tan, J., Anand, K., Mesters, J.R., Hilgenfeld, R.

To be published.

Macromolecule Content

Total Structure Weight: 20.97 kDa
Atom Count: 1,511
Modeled Residue Count: 180
Deposited Residue Count: 183
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C PROTEINASE	A	183	Coxsackievirus B3	Mutation(s): 2 EC: 3.4.22.28
UniProt
Find proteins for Q5UEA2 (Coxsackievirus B3) Explore Q5UEA2 Go to UniProtKB: Q5UEA2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5UEA2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G85 Query on G85 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-[(benzyloxy)carbonyl]-O-tert-butyl-L-seryl-N-{(2R)-5-ethoxy-5-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]pentan-2-yl}-L-phenylalaninamide C₃₅ H₄₈ N₄ O₈ JRBUWNJDFCUWEM-CRNKYVSFSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.257 (Depositor), 0.258 (DCC)
R-Value Work: 0.195 (Depositor), 0.195 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.87	α = 90
b = 69.37	β = 90
c = 75.71	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-09-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-09-19
Type: Initial release
Version 1.1: 2019-05-08
Changes: Data collection, Derived calculations, Experimental preparation, Other
Version 1.2: 2024-05-01
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.3: 2024-10-09
Changes: Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.