7JYY

Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA)pUpUpApApA (Cap-0) and S-Adenosylmethionine (SAM).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report



Literature

Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA)pUpUpApApA (Cap-0) and S-Adenosylmethionine (SAM).

Minasov, G.Shuvalova, L.Rosas-Lemus, M.Kiryukhina, O.Brunzelle, J.S.Satchell, K.J.F.Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2'-O-methyltransferaseAC300Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 2.1.1 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 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)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein 10BD141Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.19.12 (UniProt), 3.4.22 (UniProt), 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
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    RNA (5'-D(*(M7G))-R(P*AP*UP*UP*A)-3')E, F7Severe acute respiratory syndrome coronavirus 2
    Small Molecules
    Ligands 6 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SAM
    Query on SAM

    Download CCD File 
    A, C
    S-ADENOSYLMETHIONINE
    C15 H22 N6 O5 S
    MEFKEPWMEQBLKI-FCKMPRQPSA-N
     Ligand Interaction
    ZN
    Query on ZN

    Download CCD File 
    B, D
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    FMT
    Query on FMT

    Download CCD File 
    A, C
    FORMIC ACID
    C H2 O2
    BDAGIHXWWSANSR-UHFFFAOYSA-N
     Ligand Interaction
    CL
    Query on CL

    Download CCD File 
    A
    CHLORIDE ION
    Cl
    VEXZGXHMUGYJMC-UHFFFAOYSA-M
     Ligand Interaction
    MG
    Query on MG

    Download CCD File 
    A, C
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    NA
    Query on NA

    Download CCD File 
    A, C
    SODIUM ION
    Na
    FKNQFGJONOIPTF-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 166.948α = 90
    b = 166.948β = 90
    c = 98.81γ = 120
    Software Package:
    Software NamePurpose
    REFMACrefinement
    PDB_EXTRACTdata extraction
    HKL-3000data reduction
    HKL-3000data scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2020-09-16
      Type: Initial release