6GDY Oxidoreductase date Apr 24, 2018
title Crystal Structure Of 2og Oxygenase Jmjd6 (Aa 1-343) In Compl Fe(II) And 2og
authors M.S.Islam, C.J.Schofield, M.A.Mcdonough
compound source
Molecule: Bifunctional Arginine Demethylase And Lysyl-Hydro Jmjd6;
Chain: A, B
Synonym: Histone Arginine Demethylase Jmjd6,Jmjc Domain-Con Protein 6,Jumonji Domain-Containing Protein 6,Lysyl-Hydroxy Jmjd6,Peptide-Lysine 5-Dioxygenase Jmjd6,Phosphatidylserine 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 0.180 R_Free 0.216
length a length b length c angle alpha angle beta angle gamma
47.150 96.990 93.760 90.00 95.84 90.00
method X-Ray Diffractionresolution 2.04 Å
ligand AKG, EPE, FE, GOL, NA, PO4 enzyme Oxidoreductase E.C.1.14.11 BRENDA
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (129 Kb) [Save to disk]
  • Biological Unit Coordinates (6gdy.pdb1.gz) 123 Kb
  • LPC: Ligand-Protein Contacts for 6GDY
  • CSU: Contacts of Structural Units for 6GDY
  • Structure Factors (1428 Kb)
  • Retrieve 6GDY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6GDY from S2C, [Save to disk]
  • View 6GDY 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 6GDY
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6gdy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6gdy_B] [6gdy_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6GDY
  • Community annotation for 6GDY at PDBWiki (http://pdbwiki.org)

  • 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
    Bioinformatics Unit
    Weizmann Institute of Science