6FFK | pdb_00006ffk

Human apo-SOD1 bound to PtCl2(1R,2R-1,4-DACH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 
    0.256 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.226 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted D7ZClick on this verticalbar to view details

This is version 2.2 of the entry. See complete history


Literature

Interaction of Half Oxa-/Halfcis-Platin Complex with Human Superoxide Dismutase and Induced Reduction of Neurotoxicity.

Cantini, F.Calderone, V.Di Cesare Mannelli, L.Korsak, M.Gonnelli, L.Francesconi, O.Ghelardini, C.Banci, L.Nativi, C.

(2018) ACS Med Chem Lett 9: 1094-1098

  • DOI: https://doi.org/10.1021/acsmedchemlett.8b00199
  • Primary Citation of Related Structures:  
    6FFK

  • PubMed Abstract: 

    The formation of amorphous protein aggregates containing human superoxide dismutase (hSOD1) is thought to be involved in amyotrophic lateral sclerosis onset. cis -Platin inhibits the oligomerization of apo hSOD1, but its toxicity precludes any possible use in therapy. Herein, we propose a less toxic platinum complex, namely oxa/ cis -platin, as hSOD1 antiaggregation lead compound. Oxa/ cis -platin is able to interact with hSOD1 in the disulfide oxidized apo form by binding cysteine 111 (Cys111). The mild neurotoxic phenomena induced in vitro and in vivo by oxa/ cis -platin can be successfully reverted by using lypoyl derivatives, which do not interfere with the antiaggregation properties of the platin derivative.


  • Organizational Affiliation

    Dipartimento di Chimica "Ugo Schiff", University of Florence, via della Lastruccia, 3-13 50019 Sesto Fiorentino (FI), Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]A,
B,
C [auth D],
D [auth F]
153Homo sapiensMutation(s): 0 
Gene Names: SOD1
EC: 1.15.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00441 (Homo sapiens)
Explore P00441 
Go to UniProtKB:  P00441
PHAROS:  P00441
GTEx:  ENSG00000142168 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00441
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.226 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.85α = 90
b = 35.37β = 112.26
c = 114.59γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted D7ZClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-28
    Type: Initial release
  • Version 2.0: 2023-12-27
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary
  • Version 2.1: 2024-01-17
    Changes: Refinement description
  • Version 2.2: 2024-10-16
    Changes: Structure summary