5DNM Nucleosome core particle containing adducts of ruthenium(II)-toluene PTA complex date
authors Adhireksan, Z., Muhammad, R., Davey, C.A.
compound source
R_Free 0.24052
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.81
ligand MG, RAX, SO4 enzyme
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] (251 Kb) [Save to disk]
  • Biological Unit Coordinates (5dnm.pdb1.gz) 244 Kb
  • LPC: Ligand-Protein Contacts for 5DNM
  • CSU: Contacts of Structural Units for 5DNM
  • Structure Factors (2887 Kb)
  • Retrieve 5DNM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DNM from S2C, [Save to disk]
  • Re-refined 5dnm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5DNM 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 5DNM
  • 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 5dnm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5dnm_I] [5dnm_J] [5dnm_A] [5dnm_C] [5dnm_B] [5dnm] [5dnm_E] [5dnm_H] [5dnm_D] [5dnm_F] [5dnm_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5DNM: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 5DNM
  • Community annotation for 5DNM at PDBWiki (http://pdbwiki.org)

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