4C8D Oxidoreductase date Sep 30, 2013
title Crystal Structure Of Jmjc Domain Of Human Histone 3 Lysine-S Demethylase 3b (Kdm3b)
authors M.Vollmar, C.Johansson, C.Gileadi, S.Goubin, A.Szykowska, T.Kroje L.Crawley, F.Von Delft, C.H.Arrowsmith, C.Bountra, A.Edwards, U.
compound source
Molecule: Lysine-Specific Demethylase 3b
Chain: A
Fragment: Jmjc Domain, Residues 1380-1720
Synonym: Jmjc Domain Of Human Histone 3 Lysine-Specific Dem Jmjc Domain-Containing Histone Demethylation Protein 2b, Ju Domain-Containing Protein 1b, Nuclear Protein 5qnca;
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: I 2 2 2
R_factor 0.194 R_Free 0.239
length a length b length c angle alpha angle beta angle gamma
83.340 85.610 117.130 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.18 Å
ligand ACT, CL, GOL, MN, OGA enzyme Oxidoreductase E.C.1.14.11 BRENDA
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (116 Kb) [Save to disk]
  • Biological Unit Coordinates (4c8d.pdb1.gz) 111 Kb
  • LPC: Ligand-Protein Contacts for 4C8D
  • CSU: Contacts of Structural Units for 4C8D
  • Structure Factors (1169 Kb)
  • Retrieve 4C8D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4C8D from S2C, [Save to disk]
  • Re-refined 4c8d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4C8D in 3D
  • Proteopedia, because life has more than 2D.
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  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4C8D
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4C8D, from MSDmotif at EBI
  • Fold representative 4c8d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4c8d_A] [4c8d]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4C8D: [JmjC ] by SMART
  • Other resources with information on 4C8D
  • Community annotation for 4C8D at PDBWiki (http://pdbwiki.org)

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