4QBQ

Crystal structure of DNMT3a ADD domain bound to H3 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation 3D Report Full Report



Literature

Engineering of a histone-recognition domain in a de novo DNA methyltransferase alters the epigenetic landscape of ESCs

Noh, K.Wang, H.Kim, H.Wenderski, W.Fang, F.Li, C.Dewell, S.Wu, X.Ferris, A.Hughes, S.H.Zheng, D.Melnick, A.M.Patel, D.J.Li, H.Allis, C.D.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA (cytosine-5)-methyltransferase 3AAC137Homo sapiensMutation(s): 0 
Gene Names: DNMT3A
EC: 2.1.1.37
Find proteins for Q9Y6K1 (Homo sapiens)
Explore Q9Y6K1 
Go to UniProtKB:  Q9Y6K1
NIH Common Fund Data Resources
PHAROS  Q9Y6K1
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3P8Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS  P68431
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.557α = 90
b = 56.424β = 90.27
c = 57.301γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2014-05-08 
  • Released Date: 2015-05-13 
  • Deposition Author(s): Li, H., Patel, D.J.

Revision History 

  • Version 1.0: 2015-05-13
    Type: Initial release