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 In (Rsgi)
compound		source
Molecule: Lysine-Specific Histone Demethylase 1 Chain: A Fragment: Residues 172-831 Synonym: Amine Oxidase Flavin-Containing Domain Protein 2, 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 Diffraction	resolution	2.30 Å
ligand	FAD	enzyme	Oxidoreductase E.C.1 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Crystal 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 (2dw4.pdb1.gz) 106 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

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 3D motif for 2DW4, from MSDmotif at EBI

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)

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