6ZS8

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

Experimental Data Snapshot

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

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This is version 1.2 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 

    Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, FI, Italy. luigi.messori@unifi.it.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LysozymeA [auth AAA]129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A6R (Subject of Investigation/LOI)
Query on A6R
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G [auth AAA]
H [auth AAA]
I [auth AAA]
J [auth AAA]
K [auth AAA]
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
Query on DMS
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N [auth AAA]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO
Query on EDO
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D [auth AAA]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3
Query on NO3
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B [auth AAA],
C [auth AAA],
E [auth AAA],
F [auth AAA]		NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
NA
Query on NA
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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 = 78.703α = 90
b = 78.703β = 90
c = 34.462γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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