2IW5 Oxidoreductase Transcription Regulator date Jun 26, 2006
title Structural Basis For Corest-Dependent Demethylation Of Nucleosomes By The Human Lsd1 Histone Demethylase
authors M.Yang, C.B.Gocke, X.Luo, D.Borek, D.R.Tomchick, M.Machius, Z.Otwi H.Yu
compound source
Molecule: Lysine-Specific Histone Demethylase 1
Chain: A
Fragment: Swirm Domain, Amine Oxidase Domain And Linker, Re 171-836;
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: 511693
Expression_system_strain: Bl21
Expression_system_vector: Pgex-6p1
Expression_system_plasmid: Mj23

Molecule: Rest Corepressor 1
Chain: B
Fragment: Fragment Of Sant1, Linker Region And Sant2 Domain Residues 286-482;
Synonym: Protein Corest
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector: Pet-28
Expression_system_plasmid: Mj65
symmetry Space Group: I 2 2 2
R_factor 0.203 R_Free 0.212
crystal
cell
length a length b length c angle alpha angle beta angle gamma
120.354 178.222 234.932 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.57 Å
ligand CL, FAD, GOL, NH4 enzyme Oxidoreductase E.C.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceStructural basis for CoREST-dependent demethylation of nucleosomes by the human LSD1 histone demethylase., Yang M, Gocke CB, Luo X, Borek D, Tomchick DR, Machius M, Otwinowski Z, Yu H, Mol Cell. 2006 Aug 4;23(3):377-87. PMID:16885027
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (138 Kb) [Save to disk]
  • Biological Unit Coordinates (2iw5.pdb1.gz) 130 Kb
  • LPC: Ligand-Protein Contacts for 2IW5
  • CSU: Contacts of Structural Units for 2IW5
  • Likely Quarternary Molecular Structure file(s) for 2IW5
  • Structure Factors (569 Kb)
  • Retrieve 2IW5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2IW5 from S2C, [Save to disk]
  • Re-refined 2iw5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2IW5 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 2IW5
  • 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 2IW5, from MSDmotif at EBI
  • Fold representative 2iw5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2iw5_A] [2iw5_B] [2iw5]
  • SWISS-PROT database: [O60341] [Q9UKL0]
  • Domain organization of [KDM1_HUMAN] [RCOR1_HUMAN] by SWISSPFAM
  • Domain found in 2IW5: [SANT ] by SMART
  • Other resources with information on 2IW5
  • Community annotation for 2IW5 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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