5Y3Q | pdb_00005y3q

Crystal structure of SARS coronavirus papain-like protease conjugated with beta-mercaptoethanol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.184 (Depositor), 0.196 (DCC) 
  • R-Value Work: 
    0.147 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.149 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5Y3Q

This is version 1.2 of the entry. See complete history

Literature

Disulfiram can inhibit MERS and SARS coronavirus papain-like proteases via different modes

Lin, M.H.Moses, D.C.Hsieh, C.H.Cheng, S.C.Chen, Y.H.Sun, C.Y.Chou, C.Y.

(2017) Antiviral Res 150: 155-163

  • DOI: https://doi.org/10.1016/j.antiviral.2017.12.015
  • Primary Citation Related Structures: 
    5Y3E, 5Y3Q

  • PubMed Abstract: 

    Severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in southern China in late 2002 and caused a global outbreak with a fatality rate around 10% in 2003. Ten years later, a second highly pathogenic human CoV, MERS-CoV, emerged in the Middle East and has spread to other countries in Europe, North Africa, North America and Asia. As of November 2017, MERS-CoV had infected at least 2102 people with a fatality rate of about 35% globally, and hence there is an urgent need to identify antiviral drugs that are active against MERS-CoV. Here we show that a clinically available alcohol-aversive drug, disulfiram, can inhibit the papain-like proteases (PL pro s) of MERS-CoV and SARS-CoV. Our findings suggest that disulfiram acts as an allosteric inhibitor of MERS-CoV PL pro but as a competitive (or mixed) inhibitor of SARS-CoV PL pro . The phenomenon of slow-binding inhibition and the irrecoverability of enzyme activity after removing unbound disulfiram indicate covalent inactivation of SARS-CoV PL pro by disulfiram, while synergistic inhibition of MERS-CoV PL pro by disulfiram and 6-thioguanine or mycophenolic acid implies the potential for combination treatments using these three clinically available drugs.


  • Organizational Affiliation
    • Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan.

Macromolecule Content 

  • Total Structure Weight: 36.9 kDa 
  • Atom Count: 2,996 
  • Modeled Residue Count: 317 
  • Deposited Residue Count: 323 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Replicase polyprotein 1a323Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: 1a
EC: 3.4.19.12 (PDB Primary Data), 3.4.22.69 (PDB Primary Data)
UniProt
Find proteins for P0C6U8 (Severe acute respiratory syndrome coronavirus)
Explore P0C6U8 
Go to UniProtKB:  P0C6U8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6U8
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME

Query on BME



Download:Ideal Coordinates CCD File
C [auth A]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.184 (Depositor), 0.196 (DCC) 
  • R-Value Work:  0.147 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.149 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.412α = 90
b = 33.264β = 125.01
c = 90.677γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (Taiwan)Taiwan106-2320-B-010-013
Ministry of Science and Technology (Taiwan)Taiwan105-2320-B-010-012
Ministry of Science and Technology (Taiwan)Taiwan104-2320-B-010-034

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-10
    Type: Initial release
  • Version 1.1: 2018-01-17
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description