2EJR Oxidoreductase date Mar 20, 2007
title Lsd1-Tranylcypromine Complex
authors T.Sengoku, S.Mimasu, T.Umehara, S.Yokoyama, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Lysine-Specific Histone Demethylase 1
Chain: A
Fragment: Lsd1, Residues 172-833
Synonym: Flavin-Containing Amine Oxidase Domain-Containing Protein 2, Braf35-Hdac Complex Protein Bhc110;
Ec: 1.-.-.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Kiaa0601, Lsd1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: P-Gex-6p-1
symmetry Space Group: P 61 2 2
R_factor 0.204 R_Free 0.245
length a length b length c angle alpha angle beta angle gamma
185.759 185.759 108.742 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
ligand F2N enzyme Oxidoreductase E.C.1 BRENDA

Primary referenceCrystal structure of histone demethylase LSD1 and tranylcypromine at 2.25A., Mimasu S, Sengoku T, Fukuzawa S, Umehara T, Yokoyama S, Biochem Biophys Res Commun. 2008 Feb 1;366(1):15-22. Epub 2007 Nov 26. PMID:18039463
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (111 Kb) [Save to disk]
  • Biological Unit Coordinates (2ejr.pdb1.gz) 107 Kb
  • LPC: Ligand-Protein Contacts for 2EJR
  • CSU: Contacts of Structural Units for 2EJR
  • Likely Quarternary Molecular Structure file(s) for 2EJR
  • Structure Factors (239 Kb)
  • Retrieve 2EJR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2EJR from S2C, [Save to disk]
  • Re-refined 2ejr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2EJR 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 2EJR
  • 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
  • 3D motif for 2EJR, from MSDmotif at EBI
  • Fold representative 2ejr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ejr_A] [2ejr]
  • SWISS-PROT database: [O60341]
  • Domain organization of [KDM1_HUMAN] by SWISSPFAM
  • Other resources with information on 2EJR
  • Community annotation for 2EJR at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science