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

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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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13864
Protein Feature View
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  • Reference Sequence

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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

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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],
F
12synthetic 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


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