4QCL

Crystal structure of the catalytic core of human DNA polymerase alpha in ternary complex with an RNA-primed DNA template and dCTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Activity and fidelity of human DNA polymerase alpha depend on primer structure

Baranovskiy, A.G.Duong, V.Babayeva, N.D.Zhang, Y.Pavlov, Y.Anderson, K.Tahirov, T.H.

(2018) J Biol Chem 


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase alpha catalytic subunitA922Homo sapiensMutation(s): 1 
Gene Names: POLAPOLA1
EC: 2.7.7.7
Find proteins for P09884 (Homo sapiens)
Explore P09884 
Go to UniProtKB:  P09884
NIH Common Fund Data Resources
PHAROS:  P09884
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA PRIMERB11N/A
    Find similar nucleic acids by: Structure
    Entity ID: 3
    MoleculeChainsLengthOrganismImage
    DNA TEMPLATEC21N/A
    Small Molecules
    Ligands 6 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    DCP
    Query on DCP

    Download Ideal Coordinates CCD File 
    D [auth A]2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
    C9 H16 N3 O13 P3
    RGWHQCVHVJXOKC-SHYZEUOFSA-N
     Ligand Interaction
    1PE
    Query on 1PE

    Download Ideal Coordinates CCD File 
    I [auth A]PENTAETHYLENE GLYCOL
    C10 H22 O6
    JLFNLZLINWHATN-UHFFFAOYSA-N
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    F [auth A], G [auth A], K [auth B]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    EDO
    Query on EDO

    Download Ideal Coordinates CCD File 
    J [auth A]1,2-ETHANEDIOL
    C2 H6 O2
    LYCAIKOWRPUZTN-UHFFFAOYSA-N
     Ligand Interaction
    K
    Query on K

    Download Ideal Coordinates CCD File 
    H [auth A]POTASSIUM ION
    K
    NPYPAHLBTDXSSS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    E [auth A]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.20 Å
    • R-Value Free: 0.239 
    • R-Value Work: 0.210 
    • R-Value Observed: 0.210 
    • Space Group: P 32 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 140.763α = 90
    b = 140.763β = 90
    c = 181.315γ = 120
    Software Package:
    Software NamePurpose
    HKL-2000data collection
    CNSrefinement
    HKL-2000data reduction
    HKL-2000data scaling
    CNSphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2014-11-26
      Type: Initial release
    • Version 1.1: 2018-03-14
      Changes: Database references