3U4S Oxidoreductase Oxidoreductase Substrate date Oct 10, 2011
title Histone Lysine Demethylase Jmjd2a In Complex With T11c Pepti Substrate Crosslinked To N-Oxalyl-D-Cysteine
authors J.Ma, M.A.Mcdonough, C.J.Schofield
compound source
Molecule: Lysine-Specific Demethylase 4a
Chain: A, B
Fragment: Jmjc Domain, Unp Residues 1-359
Synonym: Jmjc Domain-Containing Histone Demethylation Prote Jumonji Domain-Containing Protein 2a;
Ec: 1.14.11.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Jhdm3a, Jmjd2, Jmjd2a, Kdm4a, Kiaa0677
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21 De3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic28-Bsa4

Molecule: Histone 3 Tail Analog (T11c Peptide)
Chain: C, D
Engineered: Yes

Synthetic: Yes
Other_details: This Sequence Occurs Naturally In Humans
symmetry Space Group: P 21 21 2
R_factor 0.181 R_Free 0.222
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.819 150.060 55.917 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand 08P, M3L, NI, ZN enzyme Oxidoreductase E.C.1.14.11 BRENDA
Primary referenceLinking of 2-Oxoglutarate and Substrate Binding Sites Enables Potent and Highly Selective Inhibition of JmjC Histone Demethylases., Woon EC, Tumber A, Kawamura A, Hillringhaus L, Ge W, Rose NR, Ma JH, Chan MC, Walport LJ, Che KH, Ng SS, Marsden BD, Oppermann U, McDonough MA, Schofield CJ, Angew Chem Int Ed Engl. 2012 Feb 13;51(7):1631-4. doi:, 10.1002/anie.201107833. Epub 2012 Jan 12. PMID:22241642
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (251 Kb) [Save to disk]
  • Biological Unit Coordinates (3u4s.pdb1.gz) 123 Kb
  • Biological Unit Coordinates (3u4s.pdb2.gz) 124 Kb
  • LPC: Ligand-Protein Contacts for 3U4S
  • CSU: Contacts of Structural Units for 3U4S
  • Structure Factors (744 Kb)
  • Retrieve 3U4S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3U4S from S2C, [Save to disk]
  • Re-refined 3u4s structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3U4S 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 3U4S
  • 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 3U4S, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3u4s_D] [3u4s_C] [3u4s] [3u4s_B] [3u4s_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3U4S: [JmjC] [JmjN ] by SMART
  • Other resources with information on 3U4S
  • Community annotation for 3U4S at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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