4WQN

Crystal structure of N6-methyladenosine RNA reader YTHDF2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.121 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the YTH domain of YTHDF2 reveals mechanism for recognition of N6-methyladenosine.

Zhu, T.Roundtree, I.A.Wang, P.Wang, X.Wang, L.Sun, C.Tian, Y.Li, J.He, C.Xu, Y.

(2014) Cell Res. 24: 1493-1496


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YTH domain-containing family protein 2
A, B
173Homo sapiensMutation(s): 0 
Gene Names: YTHDF2 (HGRG8)
Find proteins for Q9Y5A9 (Homo sapiens)
Go to Gene View: YTHDF2
Go to UniProtKB:  Q9Y5A9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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

Download SDF File 
Download CCD File 
B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.121 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.186 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 76.689α = 90.00
b = 76.689β = 90.00
c = 131.241γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Database references