4QBS

Crystal structure of DNMT3a ADD domain E545R mutant bound to H3T3ph peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

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 3AA138Homo sapiensMutation(s): 1 
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 H3P7Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
PL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.286α = 90
b = 57.286β = 90
c = 71.923γ = 120
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): Wang, H., Li, H.

Revision History 

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