4QGZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1021/ic5012583
  • Primary Citation of 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.


  • Organizational Affiliation

    Department of Chemistry, University of Florence , Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme C129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I83
Query on I83

Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.183 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.92α = 90
b = 77.92β = 90
c = 36.921γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2014-08-20
    Changes: Database references