2YPD Oxidoreductase date Oct 30, 2012
title Crystal Structure Of The Jumonji Domain Of Human Jumonji Dom Containing 1c Protein
authors M.Vollmar, C.Johansson, T.Krojer, G.Berridge, N.Burgess-Brown, C. Damerell, S.Froese, E.Williams, S.Goubin, D.Coutandin, F.Von Del C.H.Arrowsmith, C.Bountra, A.Edwards, U.Oppermann
compound source
Molecule: Probable Jmjc Domain-Containing Histone Demethyla Ein 2c;
Chain: A, B
Fragment: Jumonji Domain, Residues 2157-2540
Synonym: Jumonji Domain-Containing Protein 1c, Thyroid Rece Interacting Protein 8, Tr-Interacting Protein 8, Trip-8;
Ec: 1.14.11.-
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: R3-Prare2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic-Cthf
symmetry Space Group: P 2 21 21
R_factor 0.215 R_Free 0.240
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.718 112.206 165.173 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand EMT, NA enzyme Oxidoreductase E.C.1.14.11 BRENDA
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (223 Kb) [Save to disk]
  • Biological Unit Coordinates (2ypd.pdb1.gz) 110 Kb
  • Biological Unit Coordinates (2ypd.pdb2.gz) 109 Kb
  • LPC: Ligand-Protein Contacts for 2YPD
  • CSU: Contacts of Structural Units for 2YPD
  • Structure Factors (1754 Kb)
  • Retrieve 2YPD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YPD from S2C, [Save to disk]
  • Re-refined 2ypd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2YPD 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 2YPD
  • 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 2YPD, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ypd_B] [2ypd] [2ypd_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2YPD: [JmjC ] by SMART
    • Other resources with information on 2YPD
  • Community annotation for 2YPD at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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