7DA6 | pdb_00007da6

Enterovirus 71 2A Protease mutant- C110A in complex with peptide inhibitor

• PDB DOI: https://doi.org/10.2210/pdb7DA6/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Enterovirus A71, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-10-15 Released: 2021-08-25 
• Deposition Author(s): Yang, W.Z., Yuan, H.S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.244 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Efficient Strategy to Design Protease Inhibitors: Application to Enterovirus 71 2A Protease.

Chen, T., Grauffel, C., Yang, W.Z., Chen, Y.P., Yuan, H.S., Lim, C.

(2022) ACS Bio Med Chem Au 

• DOI: https://doi.org/10.1021/acsbiomedchemau.2c00001

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 15.77 kDa 
• Atom Count: 1,157 
• Modeled Residue Count: 142 
• Deposited Residue Count: 142 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyprotein	A	138	Enterovirus A71	Mutation(s): 1
UniProt
Find proteins for R9YK28 (Human enterovirus 71) Explore R9YK28  Go to UniProtKB:  R9YK28

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PHE-ARG-GLY-LYS	B [auth C]	4	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.244 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.476	α = 90
b = 44.407	β = 111.57
c = 51.369	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-08-25 
Deposition Author(s): Yang, W.Z., Yuan, H.S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2021-08-25
  Type: Initial release
  
• Version 2.0: 2021-11-10
  Type: Coordinate replacement
  Reason: Model orientation/position
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Experimental preparation, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2022-06-29
  Changes: Database references
• Version 2.2: 2023-11-29
  Changes: Data collection, Refinement description
• Version 2.3: 2024-10-23
  Changes: Structure summary