5F9X | pdb_00005f9x

X-RAY STRUCTURE OF THE ADDUCT BETWEEN HEN EGG WHITE LYSOZYME AND CISPLATIN UPON 24 HOURS OF INCUBATION AT 55 DEGREES

• PDB DOI: https://doi.org/10.2210/pdb5F9X/pdb

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


• Deposited: 2015-12-10 Released: 2016-04-13 
• Deposition Author(s): Russo Krauss, I., Ferraro, G., Pica, A., Merlino, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.248 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Effect of temperature on the interaction of cisplatin with the model protein hen egg white lysozyme.

Ferraro, G., Pica, A., Russo Krauss, I., Pane, F., Amoresano, A., Merlino, A.

(2016) J Biol Inorg Chem 21: 433-442

• PubMed: 27040953 
• DOI: https://doi.org/10.1007/s00775-016-1352-0
• Primary Citation Related Structures: 
  5F9U, 5F9X, 5FCP


• PubMed Abstract: 
  

  The products of the reaction between cisplatin (CDDP) and the model protein hen egg white lysozyme (HEWL) at 20, 37 and 55 °C in pure water were studied by UV-Vis absorption spectroscopy, intrinsic fluorescence and circular dichroism, dynamic and electrophoretic light scattering and inductively coupled plasma mass spectrometry. X-ray structures were also solved for the adducts formed at 20 and 55 °C. Data demonstrate that high temperature facilitates the formation of CDDP-HEWL adducts, where Pt atoms bind ND1 atom of His15 or NE2 atom of His15 and NH1 atom of Arg14. Our study suggests that high human body temperature (fever) could increase the rate of drug binding to proteins thus enhancing possible toxic side effects related to CDDP administration.

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Organizational Affiliation: 
• Department of Chemical Sciences, University of Naples Federico II, via Cintia, Naples, 80126, Italy.
Department of Chemical Sciences, University of Naples Federico II, via Cintia, Naples, 80126, Italy. [e-mail].
CNR Institute of Biostructure and Bioimages, via Mezzocannone 16, Naples, 80100, Italy. [e-mail].

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: 15.02 kDa 
• Atom Count: 1,164 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CPT	C [auth A], D [auth A]	Cisplatin Cl2 H6 N2 Pt LXZZYRPGZAFOLE-UHFFFAOYSA-L
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.248 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.99	α = 90
b = 77.99	β = 90
c = 36.93	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-13 
Deposition Author(s): Russo Krauss, I., Ferraro, G., Pica, A., Merlino, A.

Revision History  

• Version 1.0: 2016-04-13
  Type: Initial release
  
• Version 1.1: 2016-06-29
  Changes: Database references
• Version 1.2: 2019-10-16
  Changes: Data collection
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary