6ZS8

X-ray structure of the adduct formed upon treating lysozyme with an aged solution of arsenoplatin-1

• PDB DOI: https://doi.org/10.2210/pdb6ZS8/pdb

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


• Deposited: 2020-07-15 Released: 2020-12-23 
• Deposition Author(s): Ferraro, G., Merlino, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.239 
• R-Value Work: 0.185 

Starting Model: experimental

Literature

The first step of arsenoplatin-1 aggregation in solution unveiled by solving the crystal structure of its protein adduct.

Ferraro, G., Cirri, D., Marzo, T., Pratesi, A., Messori, L., Merlino, A.

(2021) Dalton Trans 50: 68-71

• PubMed: 33320144 
• DOI: https://doi.org/10.1039/d0dt04068a
• Primary Citation of Related Structures:  
  6ZS8


• PubMed Abstract: 
  

  Arsenoplatin-1 (AP-1) is an innovative dual-action anticancer agent that contains a platinum(ii) center coordinated to an arsenous acid moiety. We found that AP-1 spontaneously aggregates in aqueous solutions generating oligomeric species of increasing length. Afterward, we succeeded in solving the crystal structure of the adduct formed between the model protein lysozyme and an early AP-1 oligomer that turned out to be a trimer. Remarkably, this crystal structure traps an early stage of AP-1 aggregation offering detailed insight into the molecular process of the oligomer's growth.

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Organizational Affiliation: 

Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, FI, Italy. [e-mail].

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: 17.67 kDa 
• Atom Count: 1,147 
• Modelled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme	A [auth AAA]	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A6R (Subject of Investigation/LOI)	G [auth AAA], H [auth AAA], I [auth AAA], J [auth AAA], K [auth AAA], L [auth AAA], M [auth AAA]	arsenoplatin-1 C4 H8 As N2 O4 Pt OPINMBLEOXZNNE-UHFFFAOYSA-N
DMS	N [auth AAA]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	D [auth AAA]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3	B [auth AAA], C [auth AAA], E [auth AAA], F [auth AAA]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
NA	O [auth AAA]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.239 
• R-Value Work: 0.185 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.703	α = 90
b = 78.703	β = 90
c = 34.462	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: 2020-12-23 
Deposition Author(s): Ferraro, G., Merlino, A.

Revision History  

• Version 1.0: 2020-12-23
  Type: Initial release
  
• Version 1.1: 2021-01-13
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary