3KVA H3k4me3 Binding Protein, Transferase date Nov 29, 2009
title Structure Of Kiaa1718 Jumonji Domain In Complex With Alpha- Ketoglutarate
authors J.R.Horton, A.K.Upadhyay, H.H.Qi, X.Zhang, Y.Shi, X.Cheng
compound source
Molecule: Jmjc Domain-Containing Histone Demethylation Prot
Chain: A
Fragment: Unp Residues 92-488
Ec: 2.-.-.-
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Jhdm1d, Kiaa1718
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Codonplus
symmetry Space Group: P 61 2 2
R_factor 0.203 R_Free 0.269
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.100 78.100 290.800 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.79 Å
ligand AKG, FE2, OXY enzyme Transferase E.C.2 BRENDA
Primary referenceEnzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases., Horton JR, Upadhyay AK, Qi HH, Zhang X, Shi Y, Cheng X, Nat Struct Mol Biol. 2010 Jan;17(1):38-43. Epub 2009 Dec 20. PMID:20023638
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (65 Kb) [Save to disk]
  • Biological Unit Coordinates (3kva.pdb1.gz) 60 Kb
  • Biological Unit Coordinates (3kva.pdb2.gz) 117 Kb
  • LPC: Ligand-Protein Contacts for 3KVA
  • CSU: Contacts of Structural Units for 3KVA
  • Structure Factors (214 Kb)
  • Retrieve 3KVA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KVA from S2C, [Save to disk]
  • Re-refined 3kva structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3KVA 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 3KVA
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3KVA, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3kva_A] [3kva]
  • SWISS-PROT database: [Q6ZMT4]
  • Domain organization of [JHD1D_HUMAN] by SWISSPFAM
  • Domain found in 3KVA: [JmjC ] by SMART
    • Other resources with information on 3KVA
  • Community annotation for 3KVA 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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