4KGC Structural Protein Dna date Apr 29, 2013
title Nucleosome Core Particle Containing (Eta6-P-Cymene)-(1, 2- Ethylenediamine)-Ruthenium
authors Z.Adhireksan, C.A.Davey
compound source
Molecule: Histone H3.2
Chain: A, E
Engineered: Yes
Organism_scientific: Xenopus Laevis
Organism_common: Clawed Frog,Common Platanna,Platanna
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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

Organism_scientific: Xenopus Laevis
Organism_common: Clawed Frog,Common Platanna,Platanna
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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

Organism_scientific: Xenopus Laevis
Organism_common: Clawed Frog,Common Platanna,Platanna
Organism_taxid: 8355
Gene: Hist1h2aj, Loc494591
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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

Organism_scientific: Xenopus Laevis
Organism_common: Clawed Frog,Common Platanna,Platanna
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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 0.248 R_Free 0.282
crystal
cell
length a length b length c angle alpha angle beta angle gamma
106.620 109.710 181.940 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.69 Å
ligand HRU, MG, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceLigand substitutions between ruthenium-cymene compounds can control protein versus DNA targeting and anticancer activity., Adhireksan Z, Davey GE, Campomanes P, Groessl M, Clavel CM, Yu H, Nazarov AA, Yeo CH, Ang WH, Droge P, Rothlisberger U, Dyson PJ, Davey CA, Nat Commun. 2014 Mar 18;5:3462. doi: 10.1038/ncomms4462. PMID:24637564
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (249 Kb) [Save to disk]
  • Biological Unit Coordinates (4kgc.pdb1.gz) 241 Kb
  • LPC: Ligand-Protein Contacts for 4KGC
  • CSU: Contacts of Structural Units for 4KGC
  • Structure Factors (844 Kb)
  • Retrieve 4KGC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4KGC from S2C, [Save to disk]
  • Re-refined 4kgc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4KGC 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 4KGC
  • 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
  • 3D motif for 4KGC, from MSDmotif at EBI
  • Fold representative 4kgc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4kgc_I] [4kgc_D] [4kgc_A] [4kgc_G] [4kgc_C] [4kgc_H] [4kgc_E] [4kgc] [4kgc_J] [4kgc_B] [4kgc_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4KGC: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 4KGC
  • Community annotation for 4KGC at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science