4ZEE | pdb_00004zee

X-ray structure of the bis-platinum lysozyme adduct formed in the reaction between the protein and the two drugs Cisplatin and Oxaliplatin (preparation 2)

• PDB DOI: https://doi.org/10.2210/pdb4ZEE/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2015-04-20 Released: 2015-05-27 
• Deposition Author(s): Merlino, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.230 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

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

• PubMed: 25974859 
• DOI: https://doi.org/10.1039/c5dt01279a
• Primary Citation Related Structures: 
  4Z46, 4ZEE


• 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. 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.

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Organizational Affiliation: 
• Department of Pharmacy, University of Naples Federico II, via Montesano 12, 80120, Napoli, Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 15.62 kDa 
• Atom Count: 1,209 
• Modeled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PT	M [auth A]	CYCLOHEXANE-1(R),2(R)-DIAMINE-PLATINUM(II) C6 H14 N2 Pt SGLJYTWMWIAGEU-KGZKBUQUSA-N
CPT	N [auth A]	Cisplatin Cl2 H6 N2 Pt LXZZYRPGZAFOLE-UHFFFAOYSA-L
EDO	K [auth A], L [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.230 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.377	α = 90
b = 77.377	β = 90
c = 37.6	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary