5DNM Structural Protein Dna date Sep 10, 2015
title Nucleosome Core Particle Containing Adducts Of Ruthenium(II) Pta Complex
authors Z.Adhireksan, R.Muhammad, C.A.Davey
compound source
Molecule: Histone H3.2
Chain: A, E
Engineered: Yes
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid

Molecule: Histone H4
Chain: B, F
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid

Molecule: Histone H2a
Chain: C, G
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Gene: Hist1h2aj, Loc494591
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid

Molecule: Histone H2b 1.1
Chain: D, H
Synonym: H2b1.1
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid

Molecule: Dna (145-Mer)
Chain: I
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (145-Mer)
Chain: J
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.208 R_Free 0.241
crystal
cell
length a length b length c angle alpha angle beta angle gamma
106.680 109.820 182.340 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.81 Å
ligand 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] (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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