7L35

Human DNA Ligase 1 - R771W nicked DNA complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

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
GTEx  ENSG00000105486
Protein Feature View
Expand
  • 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 4 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
        TRS
        Query on TRS
        Download Ideal Coordinates CCD File 
        D
        		2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
        C4 H12 N O3
        LENZDBCJOHFCAS-UHFFFAOYSA-O        		 Ligand Interaction
        PEG
        Query on PEG
        Download Ideal Coordinates CCD File 
        A
        		DI(HYDROXYETHYL)ETHER
        C4 H10 O3
        MTHSVFCYNBDYFN-UHFFFAOYSA-N        		 Ligand Interaction
        NA
        Query on NA
        Download Ideal Coordinates CCD File 
        B
        		SODIUM ION
        Na
        FKNQFGJONOIPTF-UHFFFAOYSA-N        		 Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.00 Å
        • R-Value Free: 0.195 
        • R-Value Work: 0.163 
        • R-Value Observed: 0.164 
        • Space Group: P 21 21 21
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 71.33α = 90
        b = 100.523β = 90
        c = 116.088γ = 90
        Software Package:
        Software NamePurpose
        PHENIXrefinement
        PDB_EXTRACTdata extraction
        HKL-2000data reduction
        HKL-2000data scaling
        PHASERphasing

        Structure Validation

        View Full Validation Report


        View more in-depth experimental data

        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