4LFX | pdb_00004lfx

X-ray structure of the adduct between hen egg white lysozyme and Auoxo6, a dinuclear gold(III) complex with -dioxo bridges linking the two metal centers

• PDB DOI: https://doi.org/10.2210/pdb4LFX/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2013-06-27 Released: 2013-10-02 
• Deposition Author(s): Vergara, A., Merlino, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.281 (Depositor), 0.299 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

The mode of action of anticancer gold-based drugs: a structural perspective.

Messori, L., Scaletti, F., Massai, L., Cinellu, M.A., Gabbiani, C., Vergara, A., Merlino, A.

(2013) Chem Commun (Camb) 49: 10100-10102

• PubMed: 24045294 
• DOI: https://doi.org/10.1039/c3cc46400h
• Primary Citation Related Structures: 
  4LFP, 4LFX, 4LGK


• PubMed Abstract: 
  

  The interactions between a few representative gold-based drugs and hen egg white lysozyme were studied by X-ray crystallography. High resolution crystal structures solved for three metallodrug-protein adducts provide valuable insight into the molecular mechanism of these promising metal compounds and the inherent protein metalation processes.

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Organizational Affiliation: 
• Department of Chemistry, University of Florence, 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)

Macromolecule Content 

• Total Structure Weight: 14.66 kDa 
• Atom Count: 1,141 
• Modeled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AU	E [auth A]	GOLD ION Au ZBKIUFWVEIBQRT-UHFFFAOYSA-N
CL	B [auth A], C [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.281 (Depositor), 0.299 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.269	α = 90
b = 78.269	β = 90
c = 37.208	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-02 
Deposition Author(s): Vergara, A., Merlino, A.

Revision History  

• Version 1.0: 2013-10-02
  Type: Initial release
  
• Version 1.1: 2013-10-23
  Changes: Database references
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary