5DNN Nucleosome core particle containing adducts of gold(I)-triethylphosphane and ruthenium(II)-toluene PTA complexes date
authors Adhireksan, Z., Ma, Z., Davey, C.A.
compound source
symmetry
R_factor
R_Free 0.23648
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.80
ligand AUF, MG, RAX, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceAllosteric cross-talk in chromatin can mediate drug-drug synergy., Adhireksan Z, Palermo G, Riedel T, Ma Z, Muhammad R, Rothlisberger U, Dyson PJ, Davey CA, Nat Commun. 2017 Mar 30;8:14860. doi: 10.1038/ncomms14860. PMID:28358030
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (252 Kb) [Save to disk]
  • Biological Unit Coordinates (5dnn.pdb1.gz) 244 Kb
  • LPC: Ligand-Protein Contacts for 5DNN
  • CSU: Contacts of Structural Units for 5DNN
  • Structure Factors (1286 Kb)
  • Retrieve 5DNN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DNN from S2C, [Save to disk]
  • Re-refined 5dnn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5DNN 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 5DNN
  • 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 5dnn from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5dnn] [5dnn_C] [5dnn_E] [5dnn_D] [5dnn_F] [5dnn_A] [5dnn_J] [5dnn_H] [5dnn_G] [5dnn_I] [5dnn_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5DNN: [H2A] [H2B] [H3] [H4 ] by SMART
    • Other resources with information on 5DNN
  • Community annotation for 5DNN at PDBWiki (http://pdbwiki.org)

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