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


This is version 1.1 of the entry. See complete history


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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA (cytosine-5)-methyltransferase 3AA,
B [auth C]
137Homo sapiensMutation(s): 0 
Gene Names: DNMT3A
EC: 2.1.1.37 (PDB Primary Data), 2.1.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6K1 (Homo sapiens)
Explore Q9Y6K1 
Go to UniProtKB:  Q9Y6K1
PHAROS:  Q9Y6K1
GTEx:  ENSG00000119772 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y6K1
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3C [auth P]8Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
PHAROS:  P68431
Entity Groups  
UniProt GroupP68431
Sequence Annotations
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  • Reference Sequence
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

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-13
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Structure summary