6G5Y

The X-ray structure of the adduct formed in the reaction between lysozyme and a platinum(II) terpyridine compound (acid pH)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A case of extensive protein platination: the reaction of lysozyme with a Pt(ii)-terpyridine complex.

Ferraro, G.Marzo, T.Infrasca, T.Cilibrizzi, A.Vilar, R.Messori, L.Merlino, A.

(2018) Dalton Trans 47: 8716-8723

  • DOI: 10.1039/c8dt01254g
  • Primary Citation of Related Structures:  
    6G5V, 6G5Y

  • PubMed Abstract: 
  • An antiproliferative platinum(ii)-terpyridine complex bearing two piperidine substituents at positions 2 and 2' (compound 1, hereafter) interacts non-covalently with DNA and induces cell death through necrosis, i.e. a mode of action that is distinct from that exhibited by cisplatin (Suntharalingam, et al ...

    An antiproliferative platinum(ii)-terpyridine complex bearing two piperidine substituents at positions 2 and 2' (compound 1, hereafter) interacts non-covalently with DNA and induces cell death through necrosis, i.e. a mode of action that is distinct from that exhibited by cisplatin (Suntharalingam, et al., Metallomics, 2013, 5, 514). Here, the interaction between this Pt compound and the model protein hen egg white lysozyme (HEWL) was studied by both electrospray ionization mass spectrometry (ESI MS) and X-ray crystallography. The ESI MS data collected after 24 h protein incubation with compound 1 at two different pH values offer evidence that the metal complex degrades upon reaction with HEWL, forming adducts with 1 : 1, 2 : 1 and 3 : 1 Pt/protein ratios. Two different X-ray structures of Pt-protein adducts, obtained by the reaction of HEWL with the Pt compound under different experimental conditions and incubation times, are then reported. An unexpected extensive platination of the protein is clearly observed: Pt containing fragments bind close to the NZ atom of Lys1 and OE1 atom of Glu7, NE2 atom of His15 and NH1 atom of Arg14, ND1 atom of His15, NZ atom of Lys96, NZ atom of Lys97 and ND1 atom of Asn93, NZ atom of Lys13 and the C-terminal carboxylate, and the N-terminal amine. An additional binding site was observed close to the NZ atom of Lys33. These results suggest that both N- and C-terminal tails, as well as Lys side chains, have to be considered as potential binding sites of Pt-containing drugs. The peculiar reactivity of compound 1 with biological macromolecules could play a role in its mode of action.


    Organizational Affiliation

    Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, via Cintia, I-80126 Napoli, Italy. antonello.merlino@unina.it.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysozyme CA129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PT
Query on PT

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A]NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.49α = 90
b = 78.49β = 90
c = 36.73γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2018-07-11
    Changes: Data collection, Database references