3K2O Oxidoreductase date Sep 30, 2009
title Structure Of An Oxygenase
authors T.Krojer, M.A.Mcdonough, I.J.Clifton, M.Mantri, S.S.Ng, A.C.W.Pik D.S.Butler, C.J.Webby, G.Kochan, C.Bhatia, J.E.Bray, A.Chaikuad, O.Gileadi, F.Von Delft, J.Weigelt, C.H.Arrowsmith, C.Bountra, A.M.Edwards, C.J.Schofield, K.L.Kavanagh, U.Oppermann
compound source
Molecule: Bifunctional Arginine Demethylase And Lysyl-Hydro Jmjd6;
Chain: A, B
Fragment: Unp Residues 2-335
Synonym: Histone Arginine Demethylase Jmjd6, Peptide-Lysine Dioxygenase Jmjd6, Lysyl-Hydroxylase Jmjd6, Jmjc Domain-Con Protein 6, Jumonji Domain-Containing Protein 6, Phosphatidy Receptor, Protein Ptdsr;
Ec: 1.14.11.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Jmjd6, Kiaa0585, Ptdsr
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.192 R_Free 0.225
length a length b length c angle alpha angle beta angle gamma
49.440 102.030 98.218 90.00 95.89 90.00
method X-Ray Diffractionresolution 1.75 Å
ligand ACT, CL, GOL, MSE, NA, NI, PO4 enzyme Oxidoreductase E.C.1.14.11 BRENDA
Primary referenceCrystal Structure of the 2-Oxoglutarate- and Fe(II)-Dependent Lysyl Hydroxylase JMJD6., Mantri M, Krojer T, Bagg EA, Webby CA, Butler DS, Kochan G, Kavanagh KL, Oppermann U, McDonough MA, Schofield CJ, J Mol Biol. 2010 May 31. PMID:20685276
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (267 Kb) [Save to disk]
  • Biological Unit Coordinates (3k2o.pdb1.gz) 261 Kb
  • LPC: Ligand-Protein Contacts for 3K2O
  • CSU: Contacts of Structural Units for 3K2O
  • Structure Factors (713 Kb)
  • Retrieve 3K2O in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3K2O from S2C, [Save to disk]
  • Re-refined 3k2o structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3K2O 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 3K2O
  • 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 3K2O, from MSDmotif at EBI
  • Fold representative 3k2o from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3k2o_A] [3k2o_B] [3k2o]
  • SWISS-PROT database: [Q6NYC1]
  • Domain organization of [JMJD6_HUMAN] by SWISSPFAM
  • Domain found in 3K2O: [JmjC ] by SMART
  • Other resources with information on 3K2O
  • Community annotation for 3K2O 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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