4HON Crystal structure of human JMJD2D/KDM4D in complex with an H3K9me3 peptide and 2-oxoglutarate date
authors Krishnan, S., Trievel, R.C.
compound source
symmetry
R_factor
R_Free 0.2143
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.80
ligand AKG, M3L, NI, NO3, PDO, SCN, ZN enzyme
Primary referenceStructural and Functional Analysis of JMJD2D Reveals Molecular Basis for Site-Specific Demethylation among JMJD2 Demethylases., Krishnan S, Trievel RC, Structure. 2012 Dec 6. pii: S0969-2126(12)00415-7. doi:, 10.1016/j.str.2012.10.018. PMID:23219879
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (126 Kb) [Save to disk]
  • Biological Unit Coordinates (4hon.pdb1.gz) 62 Kb
  • Biological Unit Coordinates (4hon.pdb2.gz) 60 Kb
  • LPC: Ligand-Protein Contacts for 4HON
  • CSU: Contacts of Structural Units for 4HON
  • Structure Factors (1371 Kb)
  • Retrieve 4HON in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4HON from S2C, [Save to disk]
  • Re-refined 4hon structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4HON 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 4HON
  • 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 4HON, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4hon] [4hon_B] [4hon_G] [4hon_F] [4hon_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4HON: [JmjC] [JmjN ] by SMART
  • Other resources with information on 4HON
  • Community annotation for 4HON at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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