6BO1

Mono-adduct formed after 3 days in the reaction of dichlorido(1,3-dimethylbenzimidazol-2-ylidene)(eta6-p-cymene)ruthenium(II) with HEWL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Unexpected arene ligand exchange results in the oxidation of an organoruthenium anticancer agent: the first X-ray structure of a protein-Ru(carbene) adduct.

Sullivan, M.P.Nieuwoudt, M.K.Bowmaker, G.A.Lam, N.Y.S.Truong, D.Goldstone, D.C.Hartinger, C.G.

(2018) Chem. Commun. (Camb.) 54: 6120-6123

  • DOI: 10.1039/c8cc02433b
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The first X-ray structures of adducts formed between a RuII(N-heterocyclic carbene)(η6-p-cymene) compound and a protein are reported. Coordination to the protein induced the cleavage of the cymene ligand and EPR spectroscopy demonstrated the oxidatio ...

    The first X-ray structures of adducts formed between a RuII(N-heterocyclic carbene)(η6-p-cymene) compound and a protein are reported. Coordination to the protein induced the cleavage of the cymene ligand and EPR spectroscopy demonstrated the oxidation of the Ru centre.


    Organizational Affiliation

    School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand. c.hartinger@auckland.ac.nz and School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand. d.goldstone@auckland.ac.nz.,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand. d.goldstone@auckland.ac.nz.,School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand. c.hartinger@auckland.ac.nz.,School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand. c.hartinger@auckland.ac.nz and The Photon Factory, University of Auckland, New Zealand.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
E3D
Query on E3D

Download SDF File 
Download CCD File 
A
dichloro(1,3-dimethyl-1H-benzimidazol-3-ium-2-yl)ruthenium
dichlorido(1,3-dimethylbenzimidazol-2-ylidene)ruthenium(II)
C9 H10 Cl2 N2 Ru
AATWLMBEQHDZRT-UHFFFAOYSA-L
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.202 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.076α = 90.00
b = 78.076β = 90.00
c = 37.278γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
Aimlessdata scaling
Cootmodel building
XDSdata reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2018-06-20
    Type: Data collection, Database references