4Z46

X-ray structure of the bis-platinum lysozyme adduct formed in the reaction between the protein and the two drugs Cisplatin and Oxaliplatin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Oxaliplatin vs. cisplatin: competition experiments on their binding to lysozyme.

Marasco, D.Messori, L.Marzo, T.Merlino, A.

(2015) Dalton Trans 44: 10392-10398

  • DOI: 10.1039/c5dt01279a
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The model protein hen egg white lysozyme was challenged with oxaliplatin and cisplatin. ESI mass spectrometry, surface plasmon resonance and thermal shift analyses demonstrate the formation of a bis-platinum adduct, though in very small amounts. Crys ...

    The model protein hen egg white lysozyme was challenged with oxaliplatin and cisplatin. ESI mass spectrometry, surface plasmon resonance and thermal shift analyses demonstrate the formation of a bis-platinum adduct, though in very small amounts. Crystals of the bis-platinum adduct were obtained using two different preparations and the X-ray structures were solved at 1.85 Å and 1.95 Å resolution. Overall, the obtained data point out that, under the analyzed conditions, the two Pt drugs have similar affinities for the protein, but bind on its surface at two non-overlapping sites. In other words, these two drugs manifest a significantly different reactivity with this model protein and do not compete for the same protein binding sites.


    Organizational Affiliation

    Department of Pharmacy, University of Naples Federico II, via Montesano 12, 80120, Napoli, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CPT
Query on CPT

Download SDF File 
Download CCD File 
A
Cisplatin
diammine(dichloro)platinum
Cl2 H6 N2 Pt
LXZZYRPGZAFOLE-UHFFFAOYSA-L
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
1PT
Query on 1PT

Download SDF File 
Download CCD File 
A
CYCLOHEXANE-1(R),2(R)-DIAMINE-PLATINUM(II)
OXALIPLATIN
C6 H14 N2 Pt
SGLJYTWMWIAGEU-KGZKBUQUSA-N
 Ligand Interaction
NO3
Query on NO3

Download SDF File 
Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.155 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.318α = 90.00
b = 77.318β = 90.00
c = 37.325γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-04-01 
  • Released Date: 2015-05-27 
  • Deposition Author(s): Merlino, A.

Revision History 

  • Version 1.0: 2015-05-27
    Type: Initial release
  • Version 1.1: 2015-06-10
    Type: Database references