7L34

Human DNA Ligase 1 - R641L nicked DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report



Literature

LIG1 syndrome mutations remodel a cooperative network of ligand binding interactions to compromise ligation efficiency

Jurkiw, T.J.Tumbale, P.P.Schellenberg, M.J.Cunningham-Rundles, C.Williams, R.S.O'Brien, P.J.

To be published.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA ligase 1A647Homo sapiensMutation(s): 1 
Gene Names: LIG1
EC: 6.5.1.1
Find proteins for P18858 (Homo sapiens)
Explore P18858 
Go to UniProtKB:  P18858
NIH Common Fund Data Resources
PHAROS  P18858
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3')B11Homo sapiens
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3')C7Homo sapiens
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')D18Homo sapiens
        Small Molecules
        Ligands 1 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        AMP
        Query on AMP

        Download Ideal Coordinates CCD File 
        C
        ADENOSINE MONOPHOSPHATE
        C10 H14 N5 O7 P
        UDMBCSSLTHHNCD-KQYNXXCUSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 1.90 Å
        • R-Value Free: 0.193 
        • R-Value Work: 0.169 
        • R-Value Observed: 0.170 
        • Space Group: P 21 21 21
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 61.93α = 90
        b = 110.745β = 90
        c = 114.858γ = 90
        Software Package:
        Software NamePurpose
        PHENIXrefinement
        PDB_EXTRACTdata extraction
        HKL-2000data reduction
        HKL-2000data scaling
        PHASERphasing

        Structure Validation

        View Full Validation Report



        Entry History & Funding Information

        Deposition Data


        Funding OrganizationLocationGrant Number
        National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesZ01ES102765

        Revision History 

        • Version 1.0: 2021-01-13
          Type: Initial release