3AVS	Oxidoreductase	date	Mar 07, 2011
title	Catalytic Fragment Of Utxkdm6a Bound With N-Oxyalylglycine, Ni(II)
authors	T.Sengoku, S.Yokoyama
compound		source
Molecule: Lysine-Specific Demethylase 6a Chain: A Fragment: Unp Residues 880-1401 Synonym: Histone Demethylase Utx, Ubiquitously-Transcribed Protein On The X Chromosome, Ubiquitously-Transcribed X Chr Tetratricopeptide Repeat Protein; Ec: 1.14.11.- Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Kdm6a, Utx Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet47
symmetry	Space Group: P 21 21 21	R_factor 0.183 R_Free 0.218
crystal cell	length a length b length c angle alpha angle beta angle gamma 78.872 82.879 92.923 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.85 Å
ligand	CL, EDO, NI, OGA, ZN	enzyme	Oxidoreductase E.C.1.14.11 BRENDA
Primary reference	Structural basis for histone H3 Lys 27 demethylation by UTX/KDM6A., Sengoku T, Yokoyama S, Genes Dev. 2011 Nov 1;25(21):2266-77. Epub 2011 Oct 14. PMID:22002947

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (245 Kb) [Save to disk] Biological Unit Coordinates (3avs.pdb1.gz) 238 Kb LPC: Ligand-Protein Contacts for 3AVS CSU: Contacts of Structural Units for 3AVS Structure Factors (377 Kb) Retrieve 3AVS in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3AVS from S2C, [Save to disk] Re-refined 3avs structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3AVS 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 3AVS

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 3AVS, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3avs] [3avs_A] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 3AVS: [JmjC ] by SMART

Other resources with information on 3AVS

Community annotation for 3AVS at PDBWiki (http://pdbwiki.org)

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