3AVR Oxidoreductase Structural Protein date Mar 07, 2011
title Catalytic Fragment Of Utxkdm6a Bound With Histone H3k27me3 N-Oxyalylglycine, And 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

Molecule: Histone H3
Chain: B
Engineered: Yes

Synthetic: Yes
Other_details: Chemical Synthesis
symmetry Space Group: P 21 21 21
R_factor 0.169 R_Free 0.198
length a length b length c angle alpha angle beta angle gamma
78.905 83.081 95.057 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand CL, EDO, M3L, 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] (260 Kb) [Save to disk]
  • Biological Unit Coordinates (3avr.pdb1.gz) 252 Kb
  • LPC: Ligand-Protein Contacts for 3AVR
  • CSU: Contacts of Structural Units for 3AVR
  • Structure Factors (433 Kb)
  • Retrieve 3AVR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3AVR from S2C, [Save to disk]
  • Re-refined 3avr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3AVR 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 3AVR
  • 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 3AVR, from MSDmotif at EBI
  • Fold representative 3avr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3avr] [3avr_A] [3avr_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3AVR: [JmjC ] by SMART
  • Other resources with information on 3AVR
  • Community annotation for 3AVR at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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