2HKO Oxidoreductase date Jul 05, 2006
title Crystal Structure Of Lsd1
authors Y.Chen, Y.T.Yang, F.Wang, K.Yanane, Y.Zhang, M.Lei
compound source
Molecule: Lysine-Specific Histone Demethylase 1
Chain: A
Synonym: Amine Oxidase Flavin-Containing Domain Protein 2, Braf35-Hdac Complex Protein Bhc110;
Ec: 1.-.-.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Aof2
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b-Sumo
symmetry Space Group: P 61 2 2
R_factor 0.230 R_Free 0.283
crystal
cell
length a length b length c angle alpha angle beta angle gamma
187.113 187.113 106.581 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.80 Å
ligand FAD enzyme Oxidoreductase E.C.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of human histone lysine-specific demethylase 1 (LSD1)., Chen Y, Yang Y, Wang F, Wan K, Yamane K, Zhang Y, Lei M, Proc Natl Acad Sci U S A. 2006 Sep 19;103(38):13956-61. Epub 2006 Sep 6. PMID:16956976
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (113 Kb) [Save to disk]
  • Biological Unit Coordinates (2hko.pdb1.gz) 108 Kb
  • LPC: Ligand-Protein Contacts for 2HKO
  • CSU: Contacts of Structural Units for 2HKO
  • Likely Quarternary Molecular Structure file(s) for 2HKO
  • Structure Factors (212 Kb)
  • Retrieve 2HKO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2HKO from S2C, [Save to disk]
  • Re-refined 2hko structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2HKO 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 2HKO
  • 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 2HKO, from MSDmotif at EBI
  • Fold representative 2hko from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2hko_A] [2hko]
  • SWISS-PROT database: [O60341]
  • Domain organization of [KDM1_HUMAN] by SWISSPFAM
  • Other resources with information on 2HKO
  • Community annotation for 2HKO 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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