5NRR

Human DNMT3B PWWP domain in complex with 5-[(2-Hydroxyethyl)(propyl)amino]-1-pentanol

• PDB DOI: https://doi.org/10.2210/pdb5NRR/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-04-25 Released: 2018-05-30 
• Deposition Author(s): Rondelet, G., Wouters, J.
• Funding Organization(s): F.R.S._FNRS_Televie

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.213 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.26 kDa 
• Atom Count: 2,614 
• Modelled Residue Count: 272 
• Deposited Residue Count: 300 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA (cytosine-5)-methyltransferase 3B	A, B	150	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
96E	C [auth A], G [auth B]	5-[2-hydroxyethyl(propyl)amino]pentan-1-ol C10 H23 N O2 XJBJEDGBRSPREH-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.213 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.502	α = 90
b = 73.502	β = 90
c = 159.958	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-05-30 
Deposition Author(s): Rondelet, G., Wouters, J.

---

Funding Organization	Location	Grant Number
F.R.S._FNRS_Televie	Belgium	7.4.532.15.F.

Revision History  

• Version 1.0: 2018-05-30
  Type: Initial release
  
• Version 2.0: 2024-01-17
  Changes: Atomic model, Data collection, Database references, Refinement description