5NVO

Human DNMT3B PWWP domain in complex with choline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Targeting PWWP domain of DNA methyltransferase 3B for epigenetic cancer therapy: Identification and structural characterization of new potential protein-protein interaction inhibitors

Rondelet, G.Dal Maso, T.Maniquet, A.Themans, Q.Wouters, J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA (cytosine-5)-methyltransferase 3B
A, B
150Homo sapiensMutation(s): 0 
Gene Names: DNMT3B
EC: 2.1.1.37
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBC3 (Homo sapiens)
Explore Q9UBC3 
Go to UniProtKB:  Q9UBC3
PHAROS:  Q9UBC3
GTEx:  ENSG00000088305 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBC3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CHT
Query on CHT

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
CHOLINE ION
C5 H14 N O
OEYIOHPDSNJKLS-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.27α = 90
b = 74.27β = 90
c = 158.2γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
F.R.S._FNRS_TelevieBelgium7.4.532.15.F.

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description