5JLG | pdb_00005jlg

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

• PDB DOI: https://doi.org/10.2210/pdb5JLG/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Expression System: Bos taurus
• Mutation(s): No 


• Deposited: 2016-04-27 Released: 2016-08-03 
• Deposition Author(s): Ferraro, G., Merlino, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.236 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

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

• PubMed: 27427335 
• DOI: https://doi.org/10.1039/c6dt02380k
• Primary Citation of Related Structures:  
  5JLG


• 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 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.

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Organizational Affiliation: 
• Department of Inorganic and Analytical Chemistry, University of Jena, Germany. [e-mail].
Department of Gynecology, Jena University Hospital - Friedrich-Schiller-University Jena, Germany.
Department of Chemical Sciences, University of Naples Federico II, Italy. [e-mail].
Department of Chemical Sciences, University of Naples Federico II, Italy. [e-mail] and Institute of Biostructures and Bioimages, Naples, Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.31 kDa 
• Atom Count: 2,373 
• Modeled Residue Count: 248 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease pancreatic	A, B	124	Bos taurus	Mutation(s): 0  Gene Names: RNASE1, RNS1 EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
UniProt
Find proteins for P61823 (Bos taurus) Explore P61823  Go to UniProtKB:  P61823

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6L6	D [auth A], G [auth B]	methyl (2Z)-3-hydroxy-3-(3-hydroxyphenyl)prop-2-ene(dithioate) C10 H10 O2 S2 MOMLKGNSDNGKFJ-TWGQIWQCSA-N
RU	C [auth A], F [auth B]	RUTHENIUM ION Ru BPEVHDGLPIIAGH-UHFFFAOYSA-N
DMS	E [auth A], H [auth B], I [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.236 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.51	α = 90
b = 32.7	β = 90.03
c = 72.47	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-03 
Deposition Author(s): Ferraro, G., Merlino, A.

Revision History  

• Version 1.0: 2016-08-03
  Type: Initial release
  
• Version 1.1: 2016-08-10
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary