5XF3

Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,R-configuration)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.270
  • R-Value Work: 0.235

Literature

Macromolecules
Sequence Display for 5XF3

Classification: STRUCTURAL PROTEIN / DNA

Total Structure Weight: 200674.39


Macromolecule Entities
Molecule Chains Length Organism Details
Histone H3.1 A, E 136 Homo sapiens Gene Name(s): HIST1H3A Gene View H3FA HIST1H3B Gene View H3FL HIST1H3C Gene View H3FC HIST1H3D Gene View H3FB HIST1H3E Gene View H3FD HIST1H3F Gene View H3FI HIST1H3G Gene View H3FH HIST1H3H Gene View H3FK HIST1H3I Gene View H3FF HIST1H3J Gene View H3FJ
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H4 B, F 103 Homo sapiens Gene Name(s): HIST1H4A Gene View H4/A H4FA HIST1H4B Gene View H4/I H4FI HIST1H4C Gene View H4/G H4FG HIST1H4D Gene View H4/B H4FB HIST1H4E Gene View H4/J H4FJ HIST1H4F Gene View H4/C H4FC HIST1H4H Gene View H4/H H4FH HIST1H4I Gene View H4/M H4FM HIST1H4J Gene View H4/E H4FE HIST1H4K Gene View H4/D H4FD HIST1H4L Gene View H4/K H4FK HIST2H4A Gene View H4/N H4F2 H4FN HIST2H4 HIST2H4B Gene View H4/O H4FO HIST4H4 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H2A type 1-B/E C, G 130 Homo sapiens Gene Name(s): HIST1H2AB Gene View H2AFM HIST1H2AE Gene View H2AFA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H2B type 1-J D, H 126 Homo sapiens Gene Name(s): HIST1H2BJ Gene View H2BFR
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)
RRK
Query on RRK

G (1R,2R)-1,2-diphenylethane-1,2-diamine
C14 H16 N2
PONXTPCRRASWKW-ZIAGYGMSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

H SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
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: 2.6 Å
  • R-Value Free: 0.270
  • R-Value Work: 0.235
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 108.19 α = 90.00
b = 109.40 β = 90.00
c = 174.82 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