2Z5U	Oxidoreductase	date	Jul 17, 2007
title	Crystal Structure Of Lysine-Specific Histone Demethylase 1
authors	S.Mimasu, T.Sengoku, S.Yokoyama, Riken Structural Genomicsprot Initiative (Rsgi)
compound		source
Molecule: Lysine-Specific Histone Demethylase 1 Chain: A Fragment: Lsd1, Residues 172-833 Synonym: Flavin-Containing Amine Oxidase Domain-Containing Braf35-Hdac Complex Protein Bhc110; Ec: 1.-.-.- Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Kiaa0601, Lsd1 Expression_system: Escherichia Coli Bl21 Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pgex-Hs-6p
symmetry	Space Group: P 61 2 2	R_factor 0.225 R_Free 0.254
crystal cell	length a length b length c angle alpha angle beta angle gamma 185.759 185.759 108.742 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.25 Å
ligand	FAJ	enzyme	Oxidoreductase E.C.1 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Crystal structure of histone demethylase LSD1 and tranylcypromine at 2.25 A., 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] (109 Kb) [Save to disk] Biological Unit Coordinates (2z5u.pdb1.gz) 104 Kb LPC: Ligand-Protein Contacts for 2Z5U CSU: Contacts of Structural Units for 2Z5U Likely Quarternary Molecular Structure file(s) for 2Z5U Structure Factors (396 Kb) Retrieve 2Z5U in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2Z5U from S2C, [Save to disk] Re-refined 2z5u structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2Z5U 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 2Z5U

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 2Z5U, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2z5u_A] [2z5u] SWISS-PROT database: [O60341] Domain organization of [KDM1_HUMAN] by SWISSPFAM

Other resources with information on 2Z5U

Community annotation for 2Z5U at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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