4R3D

Crystal structure of MERS Coronavirus papain like protease

• PDB DOI: https://doi.org/10.2210/pdb4R3D/pdb

• Classification: HYDROLASE
• Organism(s): Betacoronavirus England 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-08-15 Released: 2015-08-19 
• Deposition Author(s): Kong, L.Y., Wang, Q., Ming, Z.H., Shaw, N., Sun, Y.N., Yan, L.M., Lou, Z.Y., Rao, Z.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.82 Å
• R-Value Free: 0.224 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Literature

The Crystal Structures of Middle East Respiratory Syndrome Coronavirus Papain-like Protease and Its Complex with an Inhibitor

Kong, L.Y., Wang, Q., Ming, Z.H., Sun, Y.N., Shaw, N., Yan, L.M., Lou, Z.Y., Rao, Z.H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 74.77 kDa 
• Atom Count: 5,103 
• Modelled Residue Count: 639 
• Deposited Residue Count: 672 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 3	A [auth B], B [auth A]	336	Betacoronavirus England 1	Mutation(s): 0  Gene Names: 1a EC: 3.4.19.12 (PDB Primary Data), 3.4.22.69 (PDB Primary Data)
UniProt
Find proteins for K9N638 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)) Explore K9N638  Go to UniProtKB:  K9N638

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth B], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.82 Å
• R-Value Free: 0.224 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.624	α = 90
b = 136.624	β = 90
c = 239.518	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-19 
Deposition Author(s): Kong, L.Y., Wang, Q., Ming, Z.H., Shaw, N., Sun, Y.N., Yan, L.M., Lou, Z.Y., Rao, Z.H.

Revision History  

• Version 1.0: 2015-08-19
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations