2DW4 Oxidoreductase date Aug 02, 2006
title Crystal Structure Of Human Lsd1 At 2.3 A Resolution
authors T.Sengoku, S.Yokoyama, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Lysine-Specific Histone Demethylase 1
Chain: A
Fragment: Residues 172-831
Synonym: Amine Oxidase Flavin-Containing Domain Protein 2, Braf35-Hdac Complex Protein Bhc110;
Ec: 1.-.-.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-6p-1
symmetry Space Group: P 61 2 2
R_factor 0.192 R_Free 0.226
length a length b length c angle alpha angle beta angle gamma
184.310 184.310 108.768 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
ligand FAD 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] (113 Kb) [Save to disk]
  • Biological Unit Coordinates (2dw4.pdb1.gz) 108 Kb
  • LPC: Ligand-Protein Contacts for 2DW4
  • CSU: Contacts of Structural Units for 2DW4
  • Likely Quarternary Molecular Structure file(s) for 2DW4
  • Structure Factors (464 Kb)
  • Retrieve 2DW4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DW4 from S2C, [Save to disk]
  • Re-refined 2dw4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2DW4 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 2DW4
  • 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 2DW4, from MSDmotif at EBI
  • Fold representative 2dw4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2dw4_A] [2dw4]
  • SWISS-PROT database: [O60341]
  • Domain organization of [KDM1_HUMAN] by SWISSPFAM
  • Other resources with information on 2DW4
  • Community annotation for 2DW4 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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