5ICN Transcription date Feb 23, 2016
title Hdac1:Mta1 In Complex With Inositol-6-Phosphate And A Novel Inhibitor Based On Histone H4
authors C.J.Millard, N.S.Robertson, P.J.Watson, A.G.Jameson, J.W.R.Schwa
compound source
Molecule: Metastasis-Associated Protein Mta1
Chain: A
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mta1
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293f
Expression_system_organ: Kidney
Expression_system_plasmid: Pcdna3

Molecule: Histone Deacetylase 1
Chain: B
Synonym: Hdac1
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_taxid: 9606
Expression_system_cell_line: Hek293f
Expression_system_organ: Kidney
Expression_system_plasmid: Pcdna3

Molecule: Gly-Ala-6a0-Arg-His
Chain: C
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_common: Human
Organism_taxid: 32630
Expression_system: Synthetic Construct
Expression_system_taxid: 32630
symmetry Space Group: P 32 2 1
R_factor 0.255 R_Free 0.299
crystal
cell
length a length b length c angle alpha angle beta angle gamma
107.815 107.815 134.161 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.30 Å
ligand 6A0, I6P, K, ZN enzyme Hydrolase E.C.3.5.1.98 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceInsights into the activation mechanism of class I HDAC complexes by inositol phosphates., Watson PJ, Millard CJ, Riley AM, Robertson NS, Wright LC, Godage HY, Cowley SM, Jamieson AG, Potter BV, Schwabe JW, Nat Commun. 2016 Apr 25;7:11262. doi: 10.1038/ncomms11262. PMID:27109927
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (95 Kb) [Save to disk]
  • Biological Unit Coordinates (5icn.pdb1.gz) 175 Kb
  • LPC: Ligand-Protein Contacts for 5ICN
  • CSU: Contacts of Structural Units for 5ICN
  • Structure Factors (741 Kb)
  • Retrieve 5ICN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5ICN from S2C, [Save to disk]
  • Re-refined 5icn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5ICN in 3D
  • Proteopedia, because life has more than 2D.
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  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5ICN
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5icn from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5icn_C] [5icn] [5icn_B] [5icn_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5ICN: [ELM2] [SANT ] by SMART
  • Other resources with information on 5ICN
  • Community annotation for 5ICN at PDBWiki (http://pdbwiki.org)

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