4QGZ | pdb_00004qgz

X-ray structure of the adduct formed between hen egg white lysozyme and trans-dimethylamine methylamine dichlorido platinum(II)

• PDB DOI: https://doi.org/10.2210/pdb4QGZ/pdb

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


• Deposited: 2014-05-26 Released: 2014-07-30 
• Deposition Author(s): Russo Krauss, I., Merlino, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.259 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Literature

Interactions between Anticancer trans-Platinum Compounds and Proteins: Crystal Structures and ESI-MS Spectra of Two Protein Adducts of trans-(Dimethylamino)(methylamino)dichloridoplatinum(II).

Messori, L., Marzo, T., Michelucci, E., Russo Krauss, I., Navarro-Ranninger, C., Quiroga, A.G., Merlino, A.

(2014) Inorg Chem 53: 7806-7808

• PubMed: 25025479 
• DOI: https://doi.org/10.1021/ic5012583
• Primary Citation Related Structures: 
  4QGZ, 4QH3


• PubMed Abstract: 
  

  The adducts formed between trans-(dimethylamino)(methylamino)dichloridoplatinum(II), [t-PtCl2(dma)(ma)], and two model proteins, i.e., hen egg white lysozyme and bovine pancreatic ribonuclease, were independently characterized by X-ray crystallography and electrospray ionization mass spectrometry. In these adducts, the Pt(II) center, upon chloride release, coordinates either to histidine or aspartic acid residues while both alkylamino ligands remain bound to the metal. Comparison with the cisplatin derivatives of the same proteins highlights for [t-PtCl2(dma)(ma)] a kind of biomolecular metalation remarkably different from that of cisplatin.

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Organizational Affiliation: 
• Department of Chemistry, University of Florence , Via della Lastruccia 3, 50019, Sesto Fiorentino, 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: 15.01 kDa 
• Atom Count: 1,074 
• 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  Gene Names: LYZ EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I83	B [auth A], C [auth A]	bis(chloranyl)-(dimethylamino)-(methylamino)platinum C3 H10 Cl2 N2 Pt XAGGIHWWXSGPFS-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.259 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.92	α = 90
b = 77.92	β = 90
c = 36.921	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-30 
Deposition Author(s): Russo Krauss, I., Merlino, A.

Revision History  

• Version 1.0: 2014-07-30
  Type: Initial release
  
• Version 1.1: 2014-08-20
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary