5DNN	Structural Protein Dna	date	Sep 10, 2015
title	Nucleosome Core Particle Containing Adducts Of Gold(I)- Triethylphosphane And Ruthenium(II)-Toluene Pta Complexes
authors	Z.Adhireksan, Z.Ma, 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 0.215 R_Free 0.236
crystal cell	length a length b length c angle alpha angle beta angle gamma 106.726 109.948 182.041 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.80 Å
ligand	AUF, MG, RAX, SO4	enzyme
Gene Ontology	Chain Function Process Component A, E C, G F, B H, D
Primary reference	Allosteric 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

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

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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