4LFP | pdb_00004lfp

X-ray structure of the adduct between hen egg white lysozyme and a homoleptic gold(I) complex with the saccharynate ligand

• PDB DOI: https://doi.org/10.2210/pdb4LFP/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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.236 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

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


• 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.

---

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: 1,169 
• 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	B [auth A]	GOLD ION Au ZBKIUFWVEIBQRT-UHFFFAOYSA-N
CL	C [auth A], D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.236 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.046	α = 90
b = 78.046	β = 90
c = 37.317	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNS	refinement
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: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary