6X1B

Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with the Product Nucleotide GpU.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2

Kim, Y.Wower, J.Maltseva, N.Chang, C.Jedrzejczak, R.Wilamowski, M.Kang, S.Nicolaescu,, N.Randall, G.Michalska, K.Joachimiak, A.Center for Structural Genomics of Infectious Diseases (CSGID)

(2020) Biorxiv 


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uridylate-specific endoribonucleaseAB370Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-R(*GP*U)-3')D, F2synthetic construct
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.97 Å
    • R-Value Free: 0.185 
    • R-Value Work: 0.157 
    • R-Value Observed: 0.165 
    • Space Group: P 63
    • Diffraction Data DOI: 10.18430/m36x1b Protein Diffraction
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 150.875α = 90
    b = 150.875β = 90
    c = 111.73γ = 120
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-3000data reduction
    HKL-3000data scaling
    HKL-3000phasing
    MOLREPphasing
    Cootmodel building

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

    Revision History 

    • Version 1.0: 2020-05-27
      Type: Initial release
    • Version 2.0: 2020-06-10
      Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
    • Version 2.1: 2020-08-05
      Changes: Database references, Structure summary
    • Version 2.2: 2020-12-09
      Changes: Database references