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 Diffractionresolution 1.85 Å
ligand CL, EDO, NI, OGA, ZN enzyme Oxidoreductase E.C.1.14.11 BRENDA
Primary referenceStructural 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] (252 Kb) [Save to disk]
  • Biological Unit Coordinates (3avs.pdb1.gz) 245 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
  • 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 3AVS, from MSDmotif at EBI
  • Fold representative 3avs from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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