4UC4 Replication date Aug 13, 2014
title Crystal Structure Of Hybrid Tudor Domain Of Human Lysine Dem Kdm4b
authors F.Wang, Z.Su, J.M.Denu, G.N.Phillips Jr.
compound source
Molecule: Lysine-Specific Demethylase 4b
Chain: A, B
Fragment: Tudor Domain (Unp 917-1031)
Synonym: Jmjc Domain-Containing Histone Demethylation Prote Jumonji Domain-Containing Protein 2b;
Ec: 1.14.11.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Kdm4b, Jhdm3b, Jmjd2b, Kiaa0876
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_plasmid: Pet28a
symmetry Space Group: P 31
R_factor 0.197 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
77.436 77.436 50.758 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.56 Å
ligand
enzyme Oxidoreductase E.C.1.14.11 BRENDA
Primary referenceReader domain specificity and lysine demethylase-4 family function., Su Z, Wang F, Lee JH, Stephens KE, Papazyan R, Voronina E, Krautkramer KA, Raman A, Thorpe JJ, Boersma MD, Kuznetsov VI, Miller MD, Taverna SD, Phillips GN Jr, Denu JM, Nat Commun. 2016 Nov 14;7:13387. doi: 10.1038/ncomms13387. PMID:27841353
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (4uc4.pdb1.gz) 75 Kb
  • CSU: Contacts of Structural Units for 4UC4
  • Structure Factors (156 Kb)
  • Retrieve 4UC4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4UC4 from S2C, [Save to disk]
  • Re-refined 4uc4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4UC4 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 4UC4
  • 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
  • Fold representative 4uc4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4uc4] [4uc4_B] [4uc4_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4UC4: [TUDOR ] by SMART
  • Other resources with information on 4UC4
  • Community annotation for 4UC4 at PDBWiki (http://pdbwiki.org)

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