6G5V | pdb_00006g5v

The X-ray structure of the adduct formed in the reaction between lysozyme and a platinum(II) terpyridine compound (pH 7.0)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 
    0.250 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6G5V

This is version 1.2 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: https://doi.org/10.1039/c8dt01254g
  • Primary Citation 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., 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.

Macromolecule Content 

  • Total Structure Weight: 15.62 kDa 
  • Atom Count: 1,124 
  • Modeled Residue Count: 129 
  • Deposited Residue Count: 129 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lysozyme C129Gallus 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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PT

Query on PT



Download:Ideal Coordinates CCD File
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
H [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
I [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free:  0.250 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.455α = 90
b = 79.455β = 90
c = 36.49γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2018-07-11
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary