2XXZ Oxidoreductase date Nov 12, 2010
title Crystal Structure Of The Human Jmjd3 Jumonji Domain
authors K.H.Che, W.W.Yue, T.Krojer, J.R.C.Muniz, S.S.Ng, A.Tumber, M.Danie N.Burgess-Brown, P.Savitsky, E.Ugochukwu, P.Filippakopoulos, C.Arrowsmith, J.Weigelt, A.Edwards, C.Bountra, U.Oppermann
compound source
Molecule: Lysine-Specific Demethylase 6b
Chain: A, B
Fragment: Jumonji Domain, Residues 1173-1502
Synonym: Jmjd3, Jmjc Domain-Containing Protein 3, Jumonji D Containing Protein 3, Lysine Demethylase 6b;
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)-R3-Prare2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic28-Bsa4
symmetry Space Group: P 21 21 21
R_factor 0.183 R_Free 0.216
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.757 71.431 159.698 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand 8XQ, EDO, NA, NI enzyme Oxidoreductase E.C.1.14.11 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (210 Kb) [Save to disk]
  • Biological Unit Coordinates (2xxz.pdb1.gz) 104 Kb
  • Biological Unit Coordinates (2xxz.pdb2.gz) 101 Kb
  • LPC: Ligand-Protein Contacts for 2XXZ
  • CSU: Contacts of Structural Units for 2XXZ
  • Structure Factors (3972 Kb)
  • Retrieve 2XXZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2XXZ from S2C, [Save to disk]
  • Re-refined 2xxz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2XXZ 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 2XXZ
  • 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 2XXZ, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2xxz_B] [2xxz] [2xxz_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2XXZ: [JmjC ] by SMART
  • Other resources with information on 2XXZ
  • Community annotation for 2XXZ 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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