3MNN

A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A ruthenium antimetastasis agent forms specific histone protein adducts in the nucleosome core

Wu, B.Ong, M.S.Groessl, M.Adhireksan, Z.Hartinger, C.G.Dyson, P.J.Davey, C.A.

(2011) Chemistry 17: 3562-3566


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
A, E
135Xenopus laevisMutation(s): 0 
Gene Names: HISTONE H3
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
102Xenopus laevisMutation(s): 0 
Gene Names: HISTONE H4
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G
119Xenopus laevisMutation(s): 0 
Gene Names: HISTONE H2ALOC494591
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
D, H
125Xenopus laevisMutation(s): 0 
Gene Names: HISTONE H2B
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Protein Feature View
  • Reference Sequence

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsLengthOrganism
DNA (145-MER)I145N/A

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsLengthOrganism
DNA (145-MER)J145N/A
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PTW
Query on PTW

Download CCD File 
F, G, H
1,3,5-triaza-7-phosphatricyclo[3.3.1.1~3,7~]decane
C6 H12 N3 P
FXXRPTKTLVHPAR-UHFFFAOYSA-N
 Ligand Interaction
MML
Query on MML

Download CCD File 
F, G, H
1-methyl-4-(1-methylethyl)benzene
C10 H14
HFPZCAJZSCWRBC-UHFFFAOYSA-N
 Ligand Interaction
RU
Query on RU

Download CCD File 
F, G, H
RUTHENIUM ION
Ru
BPEVHDGLPIIAGH-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
D, G, H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download CCD File 
E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.35α = 90
b = 109.86β = 90
c = 182.59γ = 90
Software Package:
Software NamePurpose
RemDAqdata collection
PHASESphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2010-04-22 
  • Released Date: 2011-04-06 
  • Deposition Author(s): Ong, M.S., Davey, C.A.

Revision History 

  • Version 1.0: 2011-04-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description