4LY1 Hydrolase Hydrolase Inhibitor date Jul 30, 2013
title Structure Of Human Hdac2 In Complex With Inhibitor 4-(Acetyl [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide
authors R.Fong, P.J.Lupardus
compound source
Molecule: Histone Deacetylase 2
Chain: A, B, C
Fragment: Core Domain (Unp Residues 8-376)
Synonym: Hd2
Ec: 3.5.1.98
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hdac2
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
symmetry Space Group: P 21 21 21
R_factor 0.169 R_Free 0.187
crystal
cell
length a length b length c angle alpha angle beta angle gamma
92.034 97.490 138.922 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.57 Å
ligand 20Y, CA, NA, NHE, PG4, ZN enzyme Hydrolase E.C.3.5.1.98 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceHistone deacetylase (HDAC) inhibitor kinetic rate constants correlate with cellular histone acetylation but not transcription and cell viability., Lauffer BE, Mintzer R, Fong R, Mukund S, Tam C, Zilberleyb I, Flicke B, Ritscher A, Fedorowicz G, Vallero R, Ortwine DF, Gunzner J, Modrusan Z, Neumann L, Koth CM, Lupardus PJ, Kaminker JS, Heise CE, Steiner P, J Biol Chem. 2013 Jul 29. PMID:23897821
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (210 Kb) [Save to disk]
  • Biological Unit Coordinates (4ly1.pdb1.gz) 71 Kb
  • Biological Unit Coordinates (4ly1.pdb2.gz) 72 Kb
  • Biological Unit Coordinates (4ly1.pdb3.gz) 69 Kb
  • LPC: Ligand-Protein Contacts for 4LY1
  • CSU: Contacts of Structural Units for 4LY1
  • Structure Factors (2772 Kb)
  • Retrieve 4LY1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4LY1 from S2C, [Save to disk]
  • Re-refined 4ly1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4LY1 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 4LY1
  • 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
  • 3D motif for 4LY1, from MSDmotif at EBI
  • Fold representative 4ly1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ly1] [4ly1_A] [4ly1_C] [4ly1_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4LY1
  • Community annotation for 4LY1 at PDBWiki (http://pdbwiki.org)

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