7PNH

X-ray structure of the adduct formed upon reaction of Pt(II) complex 2c with lysozyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.133 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Reactions with Proteins of Three Novel Anticancer Platinum(II) Complexes Bearing N-Heterocyclic Ligands.

Sacco, F.Tarchi, M.Ferraro, G.Merlino, A.Facchetti, G.Rimoldi, I.Messori, L.Massai, L.

(2021) Int J Mol Sci 22

  • DOI: https://doi.org/10.3390/ijms221910551
  • Primary Citation of Related Structures:  
    7PNH, 7PNI

  • PubMed Abstract: 

    Three novel platinum(II) complexes bearing N-heterocyclic ligands, i.e., Pt2c, Pt-IV and Pt-VIII, were previously prepared and characterized. They manifested promising in vitro anticancer properties associated with non-conventional modes of action. To gain further mechanistic insight, we have explored here the reactions of these Pt compounds with a few model proteins, i.e., hen egg white lysozyme (HEWL), bovine pancreatic ribonuclease (RNase A), horse heart cytochrome c (Cyt-c) and human serum albumin (HSA), primarily through ESI MS analysis. Characteristic and variegate patterns of reactivity were highlighted in the various cases that appear to depend both on the nature of the Pt complex and of the interacting protein. The protein-bound Pt fragments were identified. In the case of the complex Pt2c, the adducts formed upon reaction with HEWL and RNase A were further characterized by solving the respective crystal structures: this allowed us to determine the exact location of the various Pt binding sites. The implications of the obtained results are discussed in relation to the possible mechanisms of action of these innovative anticancer Pt complexes.


  • Organizational Affiliation

    Department of Chemistry, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
PT (Subject of Investigation/LOI)
Query on PT

Download Ideal Coordinates CCD File 
K [auth AAA],
N [auth AAA]
PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth AAA]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

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L [auth AAA]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
IMD (Subject of Investigation/LOI)
Query on IMD

Download Ideal Coordinates CCD File 
M [auth AAA]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
NO3
Query on NO3

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C [auth AAA]
D [auth AAA]
E [auth AAA]
F [auth AAA]
G [auth AAA]
C [auth AAA],
D [auth AAA],
E [auth AAA],
F [auth AAA],
G [auth AAA],
H [auth AAA],
I [auth AAA],
J [auth AAA]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.133 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.2α = 90
b = 77.2β = 90
c = 38.53γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-27
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.2: 2024-10-16
    Changes: Structure summary