6W8V

Crystal structure of mouse DNMT1 in complex with ACG DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.247 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

DNMT1 activity, base flipping mechanism and genome-wide DNA methylation are regulated by the DNA sequence context

Adam, S.Anteneh, H.Hornisch, M.Wagner, V.Lu, J.Radde, N.E.Bashtrykov, P.Song, J.Jeltsch, A.

(2020) Nat Commun 


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA (cytosine-5)-methyltransferase 1A, B873Mus musculusMutation(s): 0 
Gene Names: Dnmt1DnmtMet1Uim
EC: 2.1.1.37
UniProt
Find proteins for P13864 (Mus musculus)
Explore P13864 
Go to UniProtKB:  P13864
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    ACG DNA (5'-D(*CP*CP*TP*TP*CP*(5CM)P*GP*TP*AP*AP*GP*T)-3')C, D [auth E]12synthetic construct
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      ACG DNA (5'-D(*AP*CP*TP*TP*AP*(C49)P*GP*GP*AP*AP*GP*G)-3')E [auth D], F12synthetic construct
      Protein Feature View
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      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.12 Å
      • R-Value Free: 0.278 
      • R-Value Work: 0.246 
      • R-Value Observed: 0.247 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 89.24α = 90
      b = 152.149β = 94.29
      c = 96.049γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      HKL-3000data reduction
      HKL-3000data scaling
      HKL-3000phasing

      Structure Validation

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      Ligand Structure Quality Assessment  



      Entry History & Funding Information

      Deposition Data

      • Deposited Date: 2020-03-21 
      • Released Date: 2020-07-08 
      • Deposition Author(s): Anteneh, H., Song, J.

      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R35GM119721

      Revision History  (Full details and data files)

      • Version 1.0: 2020-07-08
        Type: Initial release