2OH2

Ternary Complex of Human DNA Polymerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.231 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Ternary complex of the catalytic core of human DNA polymerase Kappa with DNA and dTT

Lone, S.Townson, S.A.Uljon, S.N.Johnson, R.E.Brahma, A.Nair, D.T.Prakash, S.Prakash, L.Aggarwal, A.K.

To be published.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase kappaE [auth A], F [auth B]508Homo sapiensMutation(s): 0 
Gene Names: POLKDINB1
EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBT6 (Homo sapiens)
Explore Q9UBT6 
Go to UniProtKB:  Q9UBT6
PHAROS:  Q9UBT6
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*GP*G*GP*GP*AP*AP*GP*GP*AP*CP*CP*C)-3'C [auth P], A [auth S]13N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*TP*T*CP*CP*AP*GP*GP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'B [auth Q], D [auth T]18N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      TTP (Subject of Investigation/LOI)
      Query on TTP

      Download Ideal Coordinates CCD File 
      H [auth A], J [auth B]THYMIDINE-5'-TRIPHOSPHATE
      C10 H17 N2 O14 P3
      NHVNXKFIZYSCEB-XLPZGREQSA-N
       Ligand Interaction
      MG
      Query on MG

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

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.05 Å
      • R-Value Free: 0.294 
      • R-Value Work: 0.231 
      • Space Group: C 2 2 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 116.15α = 90
      b = 152.472β = 90
      c = 217.389γ = 90
      Software Package:
      Software NamePurpose
      CBASSdata collection
      AMoREphasing
      CNSrefinement
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

      View Full Validation Report



      Ligand Structure Quality Assessment  



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2007-02-27
        Type: Initial release
      • Version 1.1: 2008-05-01
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance
      • Version 1.3: 2018-01-24
        Changes: Structure summary