6PKZ

Structure of human DNA polymerase beta N279A complexed with 8OA in the template base paired with incoming non-hydrolyzable GTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structure of human DNA polymerase beta N279A complexed with 8OA in the template base paired with incoming non-hydrolyzable GTP

Koag, M.C.Lee, S.

To be published.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase betaA335Homo sapiensMutation(s): 1 
Gene Names: POLB
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P06746 (Homo sapiens)
Explore P06746 
Go to UniProtKB:  P06746
PHAROS:  P06746
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*CP*GP*AP*CP*(A38) P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')B [auth T]16synthetic construct
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3')C [auth P]10synthetic construct
      Protein Feature View
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      • Reference Sequence
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(P*GP*TP*CP*GP*G)-3')D5synthetic construct
        Protein Feature View
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        • Reference Sequence
        Small Molecules
        Ligands 3 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        XG4 (Subject of Investigation/LOI)
        Query on XG4

        Download Ideal Coordinates CCD File 
        H [auth A]2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine
        C10 H17 N6 O12 P3
        DWGAAFQEGIMTIA-KVQBGUIXSA-N
         Ligand Interaction
        MG
        Query on MG

        Download Ideal Coordinates CCD File 
        G [auth A]MAGNESIUM ION
        Mg
        JLVVSXFLKOJNIY-UHFFFAOYSA-N
         Ligand Interaction
        NA
        Query on NA

        Download Ideal Coordinates CCD File 
        E [auth A], F [auth A]SODIUM ION
        Na
        FKNQFGJONOIPTF-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.74 Å
        • R-Value Free: 0.249 
        • R-Value Work: 0.175 
        • R-Value Observed: 0.178 
        • Space Group: P 1 21 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 54.609α = 90
        b = 78.555β = 106.83
        c = 54.776γ = 90
        Software Package:
        Software NamePurpose
        DENZOdata reduction
        HKL-2000data scaling
        REFMACphasing
        PHENIXrefinement

        Structure Validation

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        Ligand Structure Quality Assessment  



        Entry History 

        Deposition Data

        • Deposited Date: 2019-06-30 
        • Released Date: 2020-07-01 
        • Deposition Author(s): Koag, M.C., Lee, S.

        Revision History  (Full details and data files)

        • Version 1.0: 2020-07-01
          Type: Initial release