5PIT Oxidoreductase date Feb 07, 2017
title Pandda Analysis Group Deposition -- Crystal Structure Of Jmj Initial Refinement With No Ligand Modelled (Structure 42)
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 0.160 R_Free 0.203
length a length b length c angle alpha angle beta angle gamma
70.972 70.972 149.873 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.79 Å
ligand EDO, MG, NI, OGA, SO4, ZN enzyme
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk]
  • Biological Unit Coordinates (5pit.pdb1.gz) 70 Kb
  • LPC: Ligand-Protein Contacts for 5PIT
  • CSU: Contacts of Structural Units for 5PIT
  • Structure Factors (1787 Kb)
  • Retrieve 5PIT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5PIT from S2C, [Save to disk]
  • Re-refined 5pit structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5PIT 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 5PIT
  • 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 5pit from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5pit_A] [5pit]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5PIT
  • Community annotation for 5PIT at PDBWiki (http://pdbwiki.org)

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