4MXF | pdb_00004mxf

X-ray structure of the adduct between bovine pancreatic ribonuclease and Auoxo6, a dinuclear gold(III) complex with -dioxo bridges linking the two metal centers

• PDB DOI: https://doi.org/10.2210/pdb4MXF/pdb

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


• Deposited: 2013-09-26 Released: 2013-12-25 
• Deposition Author(s): Russo Krauss, I., Vergara, A., Merlino, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Interactions of gold-based drugs with proteins: crystal structure of the adduct formed between ribonuclease A and a cytotoxic gold(iii) compound.

Messori, L., Scaletti, F., Massai, L., Cinellu, M.A., Russo Krauss, I., di Martino, G., Vergara, A., Paduano, L., Merlino, A.

(2014) Metallomics 6: 233-236

• PubMed: 24287583 
• DOI: https://doi.org/10.1039/c3mt00265a
• Primary Citation of Related Structures:  
  4MXF


• PubMed Abstract: 
  

  The reaction of Auoxo6, a dinuclear gold(III) complex, with the model protein bovine pancreatic ribonuclease is explored here by X-ray diffraction and ESI mass spectrometry. Data provide clues on the processes of adduct formation and of enzyme inhibition and, inductively, on the likely mode of action of this metallodrug.

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Organizational Affiliation: 
• Department of Chemistry "Ugo Schiff", Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), 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: 27.61 kDa 
• Atom Count: 2,015 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AU	C [auth A]	GOLD ION Au ZBKIUFWVEIBQRT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.595	α = 90
b = 31.297	β = 90.53
c = 69.027	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-25 
Deposition Author(s): Russo Krauss, I., Vergara, A., Merlino, A.

Revision History  

• Version 1.0: 2013-12-25
  Type: Initial release
  
• Version 1.1: 2014-02-12
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary