5XF6

Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having an ethylenediamine linker


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.208

Literature

Macromolecules
Sequence Display for 5XF6

Classification: STRUCTURAL PROTEIN / DNA

Total Structure Weight: 199494.41


Macromolecule Entities
Molecule Chains Length Organism Details
Histone H3.2 A, E 135 Xenopus laevis Mutation: G102A
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H4 B, F 102 Xenopus laevis Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H2A C, G 128 Xenopus laevis Mutation: ΔA127
Gene Name(s): hist1h2aj LOC494591
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H2B 1.1 D, H 125 Xenopus laevis Mutation: S29T
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (145-MER) I 145 Homo sapiens
DNA (145-MER) J 145 Homo sapiens

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
RUD
Query on RUD

G, H [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5- triaza-7-phosphaadamantane)Cl2
C16 H24 Cl2 N3 O2 P Ru
UZIJOIXYBLAWLW-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

C, G, H SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDN
Query on EDN

G ETHANE-1,2-DIAMINE
ETHYLENEDIAMINE (Synonym)
C2 H8 N2
PIICEJLVQHRZGT-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

E MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.208
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 106.84 α = 90.00
b = 109.73 β = 90.00
c = 182.53 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2017-04-07
  • Released Date: 2017-10-11
  • Deposition author(s): Ma, Z., Adhireksan, Z., Murray, B.S., Dyson, P.J., Davey, C.A.

Revision History

  • Version 1_0: 2017-10-11

    Type: Initial release