2Q8D Oxidoreductase date Jun 10, 2007
title Crystal Structure Of Jmj2d2a In Ternary Complex With Histone And Succinate
authors J.F.Couture, E.Collazo, P.Ortiz-Tello, J.S.Brunzelle, R.C.Triev
compound source
Molecule: Jmjc Domain-Containing Histone Demethylation Prot
Chain: A, B
Fragment: Jumonji Domain
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
Expression_system_taxid: 511693
Expression_system_strain: Bl-21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Histone 3 Peptide
Chain: F, G
Synonym: Peptide
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Peptide
symmetry Space Group: P 21 21 2
R_factor 0.204 R_Free 0.251
crystal
cell
length a length b length c angle alpha angle beta angle gamma
100.857 148.642 57.346 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.29 Å
ligand MLY, NI, SIN, ZN enzyme Oxidoreductase E.C.1.14.11 BRENDA
Primary referenceSpecificity and mechanism of JMJD2A, a trimethyllysine-specific histone demethylase., Couture JF, Collazo E, Ortiz-Tello PA, Brunzelle JS, Trievel RC, Nat Struct Mol Biol. 2007 Aug;14(8):689-95. Epub 2007 Jun 24. PMID:17589523
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (122 Kb) [Save to disk]
  • Biological Unit Coordinates (2q8d.pdb1.gz) 60 Kb
  • Biological Unit Coordinates (2q8d.pdb2.gz) 59 Kb
  • LPC: Ligand-Protein Contacts for 2Q8D
  • CSU: Contacts of Structural Units for 2Q8D
  • Likely Quarternary Molecular Structure file(s) for 2Q8D
  • Structure Factors (534 Kb)
  • Retrieve 2Q8D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2Q8D from S2C, [Save to disk]
  • Re-refined 2q8d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2Q8D 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 2Q8D
  • 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 2Q8D, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2q8d_F] [2q8d_G] [2q8d_A] [2q8d_B] [2q8d]
  • SWISS-PROT database: [O75164]
  • Domain organization of [KDM4A_HUMAN] by SWISSPFAM
  • Domains found in 2Q8D: [JmjC] [JmjN ] by SMART
  • Other resources with information on 2Q8D
  • Community annotation for 2Q8D 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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