6FFK | pdb_00006ffk

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

• PDB DOI: https://doi.org/10.2210/pdb6FFK/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-01-08 Released: 2018-11-28 
• Deposition Author(s): Calderone, V., Nativi, C., Cantini, F., Di Cesare Mannelli, L.

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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), 0.231 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

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

• PubMed: 30429951 
• DOI: https://doi.org/10.1021/acsmedchemlett.8b00199
• Primary Citation 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.

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Organizational Affiliation: 
• Dipartimento di Chimica "Ugo Schiff", University of Florence, via della Lastruccia, 3-13 50019 Sesto Fiorentino (FI), Italy.
CERM, University of Florence, via L. Sacconi, 6, 50019 Sesto Fiorentino (FI), Italy.
NEUROFARBA, University of Florence, v.le Pieraccini, 50, 50134 Firenze, Italy.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 64.82 kDa 
• Atom Count: 4,153 
• Modeled Residue Count: 558 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Cu-Zn]	A, B, C [auth D], D [auth F]	153	Homo sapiens	Mutation(s): 0  Gene Names: SOD1 EC: 1.15.1.1 (PDB Primary Data), 1.8 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00441 (Homo sapiens) Explore P00441  Go to UniProtKB:  P00441
PHAROS:  P00441 GTEx:  ENSG00000142168

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D7Z	E [auth A], F [auth B], G [auth D], H [auth F]	PtCl2(1(R),2(R)-DACH) C6 H12 Cl2 N2 Pt UUERTZXRKZEANK-SKSSAGQDSA-L

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), 0.231 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.85	α = 90
b = 35.37	β = 112.26
c = 114.59	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-11-28 
Deposition Author(s): Calderone, V., Nativi, C., Cantini, F., Di Cesare Mannelli, L.

Revision History  

• 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