5OY3 Oxidoreductase date Sep 07, 2017
title The Structural Basis Of The Histone Demethylase Kdm6b Histon 27 Specificity
authors S.E.Jones, L.Olsen, M.Gajhede
compound source
Molecule: Lysine-Specific Demethylase 6b
Chain: A
Synonym: Jmjc Domain-Containing Protein 3,Jumonji Domain-Co Protein 3,Lysine Demethylase 6b;
Ec: 1.14.11.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Kdm6b, Jmjd3, Kiaa0346
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108

Molecule: Histone 3 Peptide H3(17-33)A21m
Chain: B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 41 21 2
R_factor 0.165 R_Free 0.221
crystal
cell
length a length b length c angle alpha angle beta angle gamma
68.908 68.908 228.476 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.14 Å
ligand AKG, EDO, FE, TBU, ZN enzyme Oxidoreductase E.C.1.14.11 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural Basis of Histone Demethylase KDM6B Histone 3 Lysine 27 Specificity., Jones SE, Olsen L, Gajhede M, Biochemistry. 2018 Feb 6;57(5):585-592. doi: 10.1021/acs.biochem.7b01152. Epub, 2017 Dec 19. PMID:29220567
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (158 Kb) [Save to disk]
  • Biological Unit Coordinates (5oy3.pdb1.gz) 152 Kb
  • LPC: Ligand-Protein Contacts for 5OY3
  • CSU: Contacts of Structural Units for 5OY3
  • Structure Factors (658 Kb)
  • Retrieve 5OY3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5OY3 from S2C, [Save to disk]
  • View 5OY3 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 5OY3
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5oy3_A] [5oy3_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5OY3
  • Community annotation for 5OY3 at PDBWiki (http://pdbwiki.org)

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