5II3 | pdb_00005ii3

The X-ray structure of the adduct formed in the reaction between hen egg white lysozyme and compound 3, a platin(II) compound containing a O, S bidentate ligand

• PDB DOI: https://doi.org/10.2210/pdb5II3/pdb

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


• Deposited: 2016-03-01 Released: 2016-12-07 
• Deposition Author(s): Ferraro, G., Merlino, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.190 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

Platinum(ii) O,S complexes as potential metallodrugs against Cisplatin resistance.

Hildebrandt, J., Hafner, N., Gorls, H., Kritsch, D., Ferraro, G., Durst, M., Runnebaum, I.B., Merlino, A., Weigand, W.

(2016) Dalton Trans 45: 18876-18891

• PubMed: 27897281 
• DOI: https://doi.org/10.1039/c6dt01388k
• Primary Citation Related Structures: 
  5IHG, 5II3, 5ILC, 5ILF


• PubMed Abstract: 
  

  We report on platinum(ii) complexes with different cinnamic acid derivatives as ligands with cytotoxic activity against Cisplatin resistant ovarian cancer cell line subcultures of SKOV3 and A2780. A typical mechanism of action for platinum(ii) complexes as Cisplatin itself is binding to the DNA and inducing double-strand breaks. We examined the biological behavior of these potential drugs with 9-methylguanine using NMR spectroscopic methods and their DNA damage potential including γH2AX-foci analyses. X-ray diffraction methods have been used to elucidate the molecular structures of the platinum(ii) complexes. Interactions with the model protein lysozyme have been evaluated by different techniques including UV-Vis absorption spectroscopy, fluorescence and X-ray crystallography.

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Organizational Affiliation: 
• Institut für Anorganische und Analytische Chemie Friedrich-Schiller-Universität Jena Humboldtstraße 8, 07743 Jena, Germany. [e-mail].
Department of Gynecology, Jena University Hospital - Friedrich Schiller University Jena, Germany.
Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant' Angelo, Via Cintia, I-80126, Napoli, Italy.
Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant' Angelo, Via Cintia, I-80126, Napoli, Italy and CNR Institute of Biostructures and Bioimages, Via Mezzocannone 16, I-80100, Napoli, Italy. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.87 kDa 
• Atom Count: 1,172 
• 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
6B6	C [auth A]	platinum(4+) tetrahydroxide H4 O4 Pt JTAFSELAEYLDJR-UHFFFAOYSA-J
DMS	B [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.190 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.206	α = 90
b = 78.206	β = 90
c = 37.005	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: 2016-12-07 
Deposition Author(s): Ferraro, G., Merlino, A.

Revision History  

• Version 1.0: 2016-12-07
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary