5F9N

CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE ETA INSERTING dCMPNPP ACROSS A DNA TEMPLATE CONTAINING 1,N2-ETHENODEOXYGUANOSINE LESION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Bypass of the 1, N2-Ethenodeoxyguanosine Lesion by Human DNA Polymerase Eta

Patra, A.Egli, M.

To be published.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase eta A435Homo sapiensMutation(s): 0 
Gene Names: POLHRAD30RAD30AXPV
EC: 2.7.7.7
Find proteins for Q9Y253 (Homo sapiens)
Explore Q9Y253 
Go to UniProtKB:  Q9Y253
NIH Common Fund Data Resources
PHAROS:  Q9Y253
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*AP*TP*(GNE)P*AP*TP*GP*AP*CP*GP*CP*T)-3')T12synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3')P8synthetic construct
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      0KX
      Query on 0KX

      Download Ideal Coordinates CCD File 
      A
      2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine
      C9 H17 N4 O12 P3
      STYMTWKSQLVXJN-SHYZEUOFSA-N
       Ligand Interaction
      GOL
      Query on GOL

      Download Ideal Coordinates CCD File 
      A
      GLYCEROL
      C3 H8 O3
      PEDCQBHIVMGVHV-UHFFFAOYSA-N
       Ligand Interaction
      MG
      Query on MG

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

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.23 Å
      • R-Value Free: 0.210 
      • R-Value Work: 0.158 
      • R-Value Observed: 0.160 
      • Space Group: P 61
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 99.08α = 90
      b = 99.08β = 90
      c = 81.89γ = 120
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      xia2data reduction
      xia2data scaling
      PHASERphasing

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data

      • Deposited Date: 2015-12-09 
      • Released Date: 2016-12-21 
      • Deposition Author(s): Patra, A., Egli, M.

      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

      Revision History  (Full details and data files)

      • Version 1.0: 2016-12-21
        Type: Initial release
      • Version 1.1: 2017-09-27
        Changes: Author supporting evidence
      • Version 1.2: 2019-01-16
        Changes: Data collection, Source and taxonomy
      • Version 1.3: 2019-12-25
        Changes: Author supporting evidence