1N48

Y-family DNA polymerase Dpo4 in complex with DNA containing abasic lesion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A Y-family polymerase complexed with abasic lesions: catching DNA with a loaded nucleoside triphosphate

Ling, H.Boudsocq, F.Woodgate, R.Yang, W.

To be published.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase IVC [auth A]352Saccharolobus solfataricus P2Mutation(s): 0 
Gene Names: dpo4dbhSSO2448
EC: 2.7.7.7
UniProt
Find proteins for Q97W02 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97W02 
Go to UniProtKB:  Q97W02
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3'A [auth B]13N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*AP*(3DR)P*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'B [auth C]16N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      ATP (Subject of Investigation/LOI)
      Query on ATP

      Download Ideal Coordinates CCD File 
      E [auth B]ADENOSINE-5'-TRIPHOSPHATE
      C10 H16 N5 O13 P3
      ZKHQWZAMYRWXGA-KQYNXXCUSA-N
       Ligand Interaction
      CA
      Query on CA

      Download Ideal Coordinates CCD File 
      D [auth B], F [auth A], G [auth A]CALCIUM ION
      Ca
      BHPQYMZQTOCNFJ-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.20 Å
      • R-Value Free: 0.230 
      • R-Value Work: 0.204 
      • R-Value Observed: 0.204 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 75.546α = 90
      b = 88.458β = 90
      c = 92.389γ = 90
      Software Package:
      Software NamePurpose
      CNSrefinement

      Structure Validation

      View Full Validation Report



      Ligand Structure Quality Assessment  



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2004-02-24
        Type: Initial release
      • Version 1.1: 2008-04-28
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Source and taxonomy, Version format compliance