5JLG

The X-ray structure of the adduct formed in the reaction between bovine pancreatic ribonuclease and compound I, a piano-stool organometallic Ru(II) arene compound containing an O,S-chelating ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Unusual mode of protein binding by a cytotoxic pi-arene ruthenium(ii) piano-stool compound containing an O,S-chelating ligand.

Hildebrandt, J.Gorls, H.Hafner, N.Ferraro, G.Durst, M.Runnebaum, I.B.Weigand, W.Merlino, A.

(2016) Dalton Trans 45: 12283-12287

  • DOI: 10.1039/c6dt02380k

  • PubMed Abstract: 
  • A new pseudo-octahedral π-arene ruthenium(ii) piano-stool compound, containing an O,S-bidentate ligand (compound 1) and showing significant cytotoxic activity in vitro, was synthesized and characterized. In solution stability and interaction with the ...

    A new pseudo-octahedral π-arene ruthenium(ii) piano-stool compound, containing an O,S-bidentate ligand (compound 1) and showing significant cytotoxic activity in vitro, was synthesized and characterized. In solution stability and interaction with the model protein bovine pancreatic ribonuclease (RNase A) were investigated by using UV-Vis absorption spectroscopy. Its crystal structure and that of the adduct formed upon reaction with RNase A were obtained by X-ray crystallography. The comparison between the structure of purified compound 1 and that of the fragment bound to RNase A reveals an unusual mode of protein binding that includes ligand exchange and alteration of coordination sphere geometry.


    Organizational Affiliation

    Department of Inorganic and Analytical Chemistry, University of Jena, Germany. wolfgang.weigand@uni-jena.de.,Department of Gynecology, Jena University Hospital - Friedrich-Schiller-University Jena, Germany.,Department of Chemical Sciences, University of Naples Federico II, Italy. antonello.merlino@unina.it.,Department of Chemical Sciences, University of Naples Federico II, Italy. antonello.merlino@unina.it and Institute of Biostructures and Bioimages, Naples, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease pancreatic
A, B
124Bos taurusMutation(s): 0 
Gene Names: RNASE1 (RNS1)
EC: 4.6.1.18
Find proteins for P61823 (Bos taurus)
Go to Gene View: RNASE1
Go to UniProtKB:  P61823
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RU
Query on RU

Download SDF File 
Download CCD File 
A, B
RUTHENIUM ION
Ru
BPEVHDGLPIIAGH-UHFFFAOYSA-N
 Ligand Interaction
6L6
Query on 6L6

Download SDF File 
Download CCD File 
A, B
methyl (2Z)-3-hydroxy-3-(3-hydroxyphenyl)prop-2-ene(dithioate)
C10 H10 O2 S2
MOMLKGNSDNGKFJ-TWGQIWQCSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A, B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 100.510α = 90.00
b = 32.700β = 90.03
c = 72.470γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-08-10
    Type: Database references