4XDP Crystal structure of human KDM4C catalytic domain bound to tris date
authors Swinger, K.K., Boriack-Sjodin, P.A.
compound source
symmetry
R_factor
R_Free 0.2420
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.07
ligand CL, EDO, FE, PG4, PGE, TRS, ZN enzyme
Primary referenceA High-Throughput Mass Spectrometry Assay Coupled with Redox Activity Testing Reduces Artifacts and False Positives in Lysine Demethylase Screening., Wigle TJ, Swinger KK, Campbell JE, Scholle MD, Sherrill J, Admirand EA, Boriack-Sjodin PA, Kuntz KW, Chesworth R, Moyer MP, Scott MP, Copeland RA, J Biomol Screen. 2015 Mar 9. pii: 1087057115575689. PMID:25755264
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (243 Kb) [Save to disk]
  • Biological Unit Coordinates (4xdp.pdb1.gz) 120 Kb
  • Biological Unit Coordinates (4xdp.pdb2.gz) 120 Kb
  • LPC: Ligand-Protein Contacts for 4XDP
  • CSU: Contacts of Structural Units for 4XDP
  • Structure Factors (902 Kb)
  • Retrieve 4XDP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4XDP from S2C, [Save to disk]
  • Re-refined 4xdp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4XDP 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 4XDP
  • 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 4XDP, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4xdp_A] [4xdp] [4xdp_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4XDP: [JmjC] [JmjN ] by SMART
    • Other resources with information on 4XDP
  • Community annotation for 4XDP at PDBWiki (http://pdbwiki.org)

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