5YX2

Crystal structure of DNMT3A-DNMT3L in complex with DNA containing two CpG sites


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.653 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of DNMT3A-DNMT3L in complex with DNA containing two CpG sites

Zhang, Z.M.Song, J.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA (cytosine-5)-methyltransferase 3A
A, D
285Homo sapiensGene Names: DNMT3A
EC: 2.1.1.37
Find proteins for Q9Y6K1 (Homo sapiens)
Go to Gene View: DNMT3A
Go to UniProtKB:  Q9Y6K1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA (cytosine-5)-methyltransferase 3-like
B, C
208Homo sapiensGene Names: DNMT3L
Find proteins for Q9UJW3 (Homo sapiens)
Go to Gene View: DNMT3L
Go to UniProtKB:  Q9UJW3
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (25-MER)E,F25synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, D, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A, D
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PYO
Query on PYO
E, F
RNA LINKINGC9 H13 N2 O8 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.653 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.191 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 205.424α = 90.00
b = 205.424β = 90.00
c = 89.337γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
Cootmodel building
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-12-01 
  • Released Date: 2018-01-31 
  • Deposition Author(s): Zhang, Z.M., Song, J.

Revision History 

  • Version 1.0: 2018-01-31
    Type: Initial release