5PND Oxidoreductase date Feb 07, 2017
title Pandda Analysis Group Deposition -- Crystal Structure Of Jmj Initial Refinement With No Ligand Modelled (Structure 207)
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 0.155 R_Free 0.178
length a length b length c angle alpha angle beta angle gamma
71.626 71.626 150.720 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.49 Å
ligand EDO, MG, 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] (76 Kb) [Save to disk]
  • Biological Unit Coordinates (5pnd.pdb1.gz) 70 Kb
  • LPC: Ligand-Protein Contacts for 5PND
  • CSU: Contacts of Structural Units for 5PND
  • Structure Factors (2781 Kb)
  • Retrieve 5PND in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5PND from S2C, [Save to disk]
  • Re-refined 5pnd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5PND 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 5PND
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5pnd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5pnd] [5pnd_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5PND
  • Community annotation for 5PND at PDBWiki (http://pdbwiki.org)

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