5NVO | pdb_00005nvo

Human DNMT3B PWWP domain in complex with choline

• PDB DOI: https://doi.org/10.2210/pdb5NVO/pdb

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


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.244 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

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: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.47 kDa 
• Atom Count: 2,189 
• Modeled Residue Count: 256 
• 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
CHT	C [auth A], J [auth B]	CHOLINE ION C5 H14 N O OEYIOHPDSNJKLS-UHFFFAOYSA-N
SO4	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 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.27	α = 90
b = 74.27	β = 90
c = 158.2	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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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 1.1: 2019-10-16
  Changes: Data collection
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description