4L55 | pdb_00004l55

X-ray structure of the adduct between bovine pancreatic ribonuclease and AziRu

• PDB DOI: https://doi.org/10.2210/pdb4L55/pdb

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


• Deposited: 2013-06-10 Released: 2014-01-29 
• Deposition Author(s): Vergara, A., Russo Krauss, I., Merlino, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.244 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

Investigating the ruthenium metalation of proteins: X-ray structure and Raman microspectroscopy of the complex between RNase A and AziRu.

Vergara, A., Russo Krauss, I., Montesarchio, D., Paduano, L., Merlino, A.

(2013) Inorg Chem 52: 10714-10716

• PubMed: 24093479 
• DOI: https://doi.org/10.1021/ic401494v
• Primary Citation Related Structures: 
  4L55


• PubMed Abstract: 
  

  A Raman-assisted crystallographic study on the adduct between AziRu, a Ru(III) complex with high antiproliferative activity, and RNase A is presented. The protein structure is not perturbed significantly by the Ru label. The metal coordinates to ND atoms of His105 or of His119 imidazole rings, losing all of its original ligands but retaining octahedral, although distorted, coordination geometry. The AziRu binding inactivates the enzyme, suggesting that its antitumor action can be exerted by a mechanism of competitive inhibition.

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Organizational Affiliation: 
• Department of Chemical Sciences, University of Naples Federico II , Napoli, Italy.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.62 kDa 
• Atom Count: 2,232 
• 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  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RU	C [auth A], D [auth B]	RUTHENIUM ION Ru BPEVHDGLPIIAGH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.244 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.104	α = 90
b = 32.532	β = 90.41
c = 72.484	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-29 
Deposition Author(s): Vergara, A., Russo Krauss, I., Merlino, A.

Revision History  

• Version 1.0: 2014-01-29
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary