6T49

3C-like protease from Southampton virus complexed with FMOPL000582a.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report



Literature

In crystallo-screening for discovery of human norovirus 3C-like protease inhibitors.

Guo, J.Douangamath, A.Song, W.Coker, A.R.Chan, A.W.E.Wood, S.P.Cooper, J.B.Resnick, E.London, N.Delft, F.V.

(2020) J Struct Biol X 4: 100031-100031

  • DOI: 10.1016/j.yjsbx.2020.100031
  • Primary Citation of Related Structures:  
    6TGL, 6T1Q, 6T2I, 6T3G, 6T2X, 6T4S, 6T4E, 6T49, 6T5R, 6T5D

  • PubMed Abstract: 
  • Outbreaks of human epidemic nonbacterial gastroenteritis are mainly caused by noroviruses. Viral replication requires a 3C-like cysteine protease (3CL pro ) which processes the 200 kDa viral polyprotein into six functional proteins. The 3C ...

    Outbreaks of human epidemic nonbacterial gastroenteritis are mainly caused by noroviruses. Viral replication requires a 3C-like cysteine protease (3CL pro ) which processes the 200 kDa viral polyprotein into six functional proteins. The 3CL pro has attracted much interest due to its potential as a target for antiviral drugs. A system for growing high-quality crystals of native Southampton norovirus 3CL pro (SV3CP) has been established, allowing the ligand-free crystal structure to be determined to 1.3 Å in a tetrameric state. This also allowed crystal-based fragment screening to be performed with various compound libraries, ultimately to guide drug discovery for SV3CP. A total of 19 fragments were found to bind to the protease out of the 844 which were screened. Two of the hits were located at the active site of SV3CP and showed good inhibitory activity in kinetic assays. Another 5 were found at the enzyme's putative RNA-binding site and a further 11 were located in the symmetric central cavity of the tetramer.


    Organizational Affiliation

    Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Genome polyproteinA172Southampton virus (serotype 3)Mutation(s): 0 
Gene Names: ORF1
EC: 3.6.1.15 (PDB Primary Data), 3.4.22.66 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
Find proteins for Q04544 (Southampton virus (strain GI/Human/United Kingdom/Southampton/1991))
Explore Q04544 
Go to UniProtKB:  Q04544
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Genome polyproteinB170Southampton virus (serotype 3)Mutation(s): 0 
Gene Names: ORF1
EC: 3.6.1.15 (PDB Primary Data), 3.4.22.66 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
Find proteins for Q04544 (Southampton virus (strain GI/Human/United Kingdom/Southampton/1991))
Explore Q04544 
Go to UniProtKB:  Q04544
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MH5
Query on MH5

Download CCD File 
A
3-[(5-methylthiophen-2-yl)methylamino]benzoic acid
C13 H13 N O2 S
PMNTXRWWXFDZFS-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A, B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.157 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.704α = 90
b = 89.303β = 96.52
c = 60.701γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2019-10-13 
  • Released Date: 2020-08-19 
  • Deposition Author(s): Guo, J., Cooper, J.B.

Revision History 

  • Version 1.0: 2020-08-19
    Type: Initial release