6Z2J Gene Regulation date May 16, 2020
title The Structure Of The Dimeric Hdac1mideasdnttip1 Midac Deac Complex
authors L.Fairall, A.Saleh, T.J.Ragan, C.J.Millard, C.G.Savva, J.W.R.Schw
compound source
Molecule: Histone Deacetylase 1
Chain: C, E
Synonym: Hd1
Ec: 3.5.1.98
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hdac1, Rpd3l1
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293f
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcdna3

Molecule: Deoxynucleotidyltransferase Terminal-Interacting
Chain: A, B
Synonym: Terminal Deoxynucleotidyltransferase-Interacting F Tdt-Interacting Factor 1;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dnttip1, C20orf167, Tdif1
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293f
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcdna3

Molecule: Mitotic Deacetylase-Associated Sant Domain Protei
Chain: F, D
Synonym: Elm2 And Sant Domain-Containing Protein 1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mideas, C14orf117, C14orf43, Elmsan1
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293f
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcdna3
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 4.00 Å
ligand IHP, K, ZN enzyme Hydrolase E.C.3.5.1.98 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
C, E
  • histone deacetylase activity...


  • Primary referenceThe MiDAC histone deacetylase complex is essential for embryonic development and has a unique multivalent structure., Turnbull RE, Fairall L, Saleh A, Kelsall E, Morris KL, Ragan TJ, Savva CG, Chandru A, Millard CJ, Makarova OV, Smith CJ, Roseman AM, Fry AM, Cowley SM, Schwabe JWR, Nat Commun. 2020 Jun 26;11(1):3252. doi: 10.1038/s41467-020-17078-8. PMID:32591534
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (339 Kb) [Save to disk]
  • Biological Unit Coordinates (6z2j.pdb1.gz) 325 Kb
  • LPC: Ligand-Protein Contacts for 6Z2J
  • CSU: Contacts of Structural Units for 6Z2J
  • Retrieve 6Z2J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6Z2J from S2C, [Save to disk]
  • View 6Z2J 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 6Z2J
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6z2j_D] [6z2j_C] [6z2j_B] [6z2j_E] [6z2j_F] [6z2j_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6Z2J
  • Community annotation for 6Z2J at PDBWiki (http://pdbwiki.org)

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