2XDP Oxidoreductase date May 06, 2010
title Crystal Structure Of The Tudor Domain Of Human Jmjd2c
authors W.W.Yue, C.Gileadi, T.Krojer, H.Weisbach, E.Ugochukwu, M.Daniel, C.Phillips, A.Chaikuad, F.Von Delft, C.Allerston, C.Arrowsmith, J.Weigelt, A.Edwards, C.Bountra, U.Oppermann
compound source
Molecule: Lysine-Specific Demethylase 4c
Chain: A
Fragment: Tudor Domain, Residues 875-995
Synonym: Jmjd2c, Jmjc Domain-Containing Histone Demethylati 3c, Jumonji Domain-Containing Protein 2c, Gene Amplified In Cell Carcinoma 1 Protein, Gasc-1 Protein;
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
Expression_system_vector: Pnic28-Bsa4
symmetry Space Group: I 2 2 2
R_factor 0.186 R_Free 0.206
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.815 79.646 81.614 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.56 Å
ligand SO4 enzyme Oxidoreductase E.C.1.14.11 BRENDA
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (49 Kb) [Save to disk]
  • Biological Unit Coordinates (2xdp.pdb1.gz) 85 Kb
  • LPC: Ligand-Protein Contacts for 2XDP
  • CSU: Contacts of Structural Units for 2XDP
  • Structure Factors (1203 Kb)
  • Retrieve 2XDP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2XDP from S2C, [Save to disk]
  • Re-refined 2xdp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2XDP 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 2XDP
  • 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 2XDP, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2xdp] [2xdp_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2XDP: [TUDOR ] by SMART
    • Other resources with information on 2XDP
  • Community annotation for 2XDP at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science