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
crystal
cell
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
Gene
Ontology
ChainFunctionProcessComponent
A


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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