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

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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