2OT7 Oxidoreductase date Feb 07, 2007
title Crystal Structure Of Jmjd2a Complexed With Histone H3 Peptid Monomethylated At Lys9
authors K.L.Kavanagh, S.S.Ng, E.Pilka, M.A.Mcdonough, P.Savitsky, F.Von D C.H.Arrowsmith, J.Weigelt, A.Edwards, M.Sundstrom, C.J.Schofiel U.Oppermann, Structural Genomics Consortium (Sgc)
compound source
Molecule: Jmjc Domain-Containing Histone Demethylation Prot
Chain: A, B
Synonym: Jumonji Domain-Containing Protein 2a
Ec: 1.14.11.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Jmjd2a, Jhdm3a, Jmjd2, Kiaa0677
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic28-Bsa4

Molecule: Histone 3 K9 Monomethyl
Chain: C, D
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic H3 Peptide Monomethylated At K9. I Sequence Is Based On Human Histone H3 Fragment (Residues 7- Hist1h3a
symmetry Space Group: P 21 21 2
R_factor 0.187 R_Free 0.241
crystal
cell
length a length b length c angle alpha angle beta angle gamma
101.209 149.842 57.470 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.14 Å
ligand ALY, MLZ, NI, OGA, ZN BindingDB enzyme Oxidoreductase E.C.1.14.11 BRENDA
Primary referenceCrystal structures of histone demethylase JMJD2A reveal basis for substrate specificity., Ng SS, Kavanagh KL, McDonough MA, Butler D, Pilka ES, Lienard BM, Bray JE, Savitsky P, Gileadi O, von Delft F, Rose NR, Offer J, Scheinost JC, Borowski T, Sundstrom M, Schofield CJ, Oppermann U, Nature. 2007 Jul 5;448(7149):87-91. Epub 2007 Jun 24. PMID:17589501
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (127 Kb) [Save to disk]
  • Biological Unit Coordinates (2ot7.pdb1.gz) 61 Kb
  • Biological Unit Coordinates (2ot7.pdb2.gz) 62 Kb
  • LPC: Ligand-Protein Contacts for 2OT7
  • CSU: Contacts of Structural Units for 2OT7
  • Likely Quarternary Molecular Structure file(s) for 2OT7
  • Structure Factors (2209 Kb)
  • Retrieve 2OT7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2OT7 from S2C, [Save to disk]
  • Re-refined 2ot7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2OT7 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 2OT7
  • 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 2OT7, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ot7_D] [2ot7] [2ot7_A] [2ot7_B] [2ot7_C]
  • SWISS-PROT database: [O75164]
  • Domain organization of [KDM4A_HUMAN] by SWISSPFAM
  • Domains found in 2OT7: [JmjC] [JmjN ] by SMART
  • Other resources with information on 2OT7
  • Community annotation for 2OT7 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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