3HWT

Ternary complex of DNA polymerase lambda bound to a two nucleotide gapped DNA substrate with a scrunched dA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Scrunching during DNA repair synthesis

Garcia-Diaz, M.Bebenek, K.Larrea, A.A.Havener, J.M.Perera, L.Krahn, J.M.Pedersen, L.C.Ramsden, D.A.Kunkel, T.A.

To be published.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase lambda A335Homo sapiensMutation(s): 1 
Gene Names: POLL
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
Find proteins for Q9UGP5 (Homo sapiens)
Explore Q9UGP5 
Go to UniProtKB:  Q9UGP5
NIH Common Fund Data Resources
PHAROS:  Q9UGP5
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*GP*GP*CP*AP*AP*AP*TP*AP*CP*TP*G)-3'T12N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*AP*GP*TP*AP*(2DT))-3'P6N/A
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        5'-D(P*GP*CP*CP*G)-3'D4N/A
        Small Molecules
        Ligands 4 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        D3T
        Query on D3T

        Download Ideal Coordinates CCD File 
        A
        2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
        C10 H17 N2 O13 P3
        URGJWIFLBWJRMF-JGVFFNPUSA-N
         Ligand Interaction
        EDO
        Query on EDO

        Download Ideal Coordinates CCD File 
        A
        1,2-ETHANEDIOL
        C2 H6 O2
        LYCAIKOWRPUZTN-UHFFFAOYSA-N
         Ligand Interaction
        MG
        Query on MG

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

        Download Ideal Coordinates CCD File 
        A
        SODIUM ION
        Na
        FKNQFGJONOIPTF-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 1.95 Å
        • R-Value Free: 0.261 
        • R-Value Work: 0.228 
        • Space Group: P 21 21 21
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 56.023α = 90
        b = 68.328β = 90
        c = 137.85γ = 90
        Software Package:
        Software NamePurpose
        DENZOdata reduction
        SCALEPACKdata scaling
        MOLREPphasing
        CNSrefinement
        PDB_EXTRACTdata extraction
        HKL-2000data collection

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History 

        • Version 1.0: 2009-08-25
          Type: Initial release
        • Version 1.1: 2011-07-13
          Changes: Version format compliance
        • Version 1.2: 2013-09-25
          Changes: Derived calculations
        • Version 1.3: 2017-11-01
          Changes: Refinement description