5PHN Oxidoreductase date Feb 07, 2017
title Pandda Analysis Group Deposition -- Crystal Structure Of Jmj Complex With N09522a
authors N.M.Pearce, T.Krojer, R.Talon, A.R.Bradley, M.Fairhead, R.Sethi, N E.Maclean, P.Collins, J.Brandao-Neto, A.Douangamath, Z.Renjie, A M.Vollmar, J.Ng, A.Szykowska, N.Burgess-Brown, P.E.Brennan, O.Co U.Oppermann, C.Bountra, C.H.Arrowsmith, A.Edwards, F.Von Delft
compound source
Molecule: Lysine-Specific Demethylase 4d
Chain: A
Synonym: Jmjc Domain-Containing Histone Demethylation Prote Jumonji Domain-Containing Protein 2d;
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Kdm4d, Jhdm3d, Jmjd2d
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 43 21 2
R_factor 0.134 R_Free 0.167
crystal
cell
length a length b length c angle alpha angle beta angle gamma
71.657 71.657 150.715 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.29 Å
ligand AC6, EDO, NI, OGA, SO4, ZN enzyme
Primary referenceA multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density., Pearce NM, Krojer T, Bradley AR, Collins P, Nowak RP, Talon R, Marsden BD, Kelm S, Shi J, Deane CM, von Delft F, Nat Commun. 2017 Apr 24;8:15123. doi: 10.1038/ncomms15123. PMID:28436492
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (147 Kb) [Save to disk]
  • Biological Unit Coordinates (5phn.pdb1.gz) 141 Kb
  • LPC: Ligand-Protein Contacts for 5PHN
  • CSU: Contacts of Structural Units for 5PHN
  • Structure Factors (10156 Kb)
  • Retrieve 5PHN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5PHN from S2C, [Save to disk]
  • Re-refined 5phn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5PHN 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 5PHN
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5phn_A] [5phn]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5PHN
  • Community annotation for 5PHN at PDBWiki (http://pdbwiki.org)

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