Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 14863.67 
• Atom Count: 1081 
• Residue Count: 129 
• Unique protein chains: 1

5ILC

The X-ray structure of the adduct formed in the reaction between hen egg white lysozyme a compound 2, a platin(II) compound containing a O, S bidentate ligand

• DOI: 10.2210/pdb5ILC/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus


• Deposited: 2016-03-04 Released: 2016-12-07 
• Deposition Author(s): Merlino, A., Ferraro, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.211 
• R-Value Work: 0.158 

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: 10.1039/c6dt01388k
• Primary Citation of Related Structures:  
  5ILF, 5II3, 5IHG


• 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 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].,Department of Gynecology, Jena University Hospital - Friedrich Schiller University Jena, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Lysozyme C	A	129	Gallus gallus	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
PT	A	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
DMS	A	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.211 
• R-Value Work: 0.158 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 77.407	α = 90.00
b = 77.407	β = 90.00
c = 37.347	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-03-04 
• Released Date: 2016-12-07 
• Deposition Author(s): Merlino, A., Ferraro, G.

Revision History 

• Version 1.0: 2016-12-07
  Type: Initial release