4RDN Structure of YTH-YTHDF2 in complex with m6A date
authors Li, F.D., Zhao, D.B., Wu, J.H., Shi, Y.Y.
compound source
symmetry
R_factor
R_Free 0.2699
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.10
ligand 6MD, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructure of the YTH domain of human YTHDF2 in complex with an m(6)A mononucleotide reveals an aromatic cage for m(6)A recognition., Li F, Zhao D, Wu J, Shi Y, Cell Res. 2014 Dec;24(12):1490-2. doi: 10.1038/cr.2014.153. Epub 2014 Nov 21. PMID:25412658
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (60 Kb) [Save to disk]
  • Biological Unit Coordinates (4rdn.pdb1.gz) 29 Kb
  • Biological Unit Coordinates (4rdn.pdb2.gz) 28 Kb
  • LPC: Ligand-Protein Contacts for 4RDN
  • CSU: Contacts of Structural Units for 4RDN
  • Structure Factors (466 Kb)
  • Retrieve 4RDN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4RDN from S2C, [Save to disk]
  • Re-refined 4rdn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4RDN in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 4RDN
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4RDN, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4rdn_A] [4rdn] [4rdn_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4RDN
  • Community annotation for 4RDN at PDBWiki (http://pdbwiki.org)

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