3RE0 | pdb_00003re0

Crystal structure of human apo Cu,Zn superoxide dismutase (SOD1) complexed with cisplatin

• PDB DOI: https://doi.org/10.2210/pdb3RE0/pdb

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


• Deposited: 2011-04-02 Released: 2012-04-25 
• Deposition Author(s): Bertini, I., Blazevits, O., Calderone, V., Jaifei, M., Vieru, M., Amori, I., Cozzolino, M., Carri, M.T., Banci, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.290 (Depositor), 0.293 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Interaction of cisplatin with human superoxide dismutase.

Banci, L., Bertini, I., Blazevits, O., Calderone, V., Cantini, F., Mao, J., Trapananti, A., Vieru, M., Amori, I., Cozzolino, M., Carri, M.T.

(2012) J Am Chem Soc 134: 7009-7014

• PubMed: 22471402 
• DOI: https://doi.org/10.1021/ja211591n
• Primary Citation Related Structures: 
  3RE0


• PubMed Abstract: 
  

  cis-Diamminedichloroplatinum(II) (cisplatin) is able to interact with human superoxide dismutase (hSOD1) in the disulfide oxidized apo form with a dissociation constant of 37 ± 3 μM through binding cysteine 111 (Cys111) located at the edge of the subunit interface. It also binds to Cu(2)-Zn(2) and Zn(2)-Zn(2) forms of hSOD1. Cisplatin inhibits aggregation of demetalated oxidized hSOD1, and it is further able to dissolve and monomerize oxidized hSOD1 oligomers in vitro and in cell, thus indicating its potential as a leading compound for amyotrophic lateral sclerosis.

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Organizational Affiliation: 
• Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy. [e-mail]

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: 64.21 kDa 
• Atom Count: 4,143 
• Modeled Residue Count: 555 
• 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, D	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
CPT	E [auth B], F [auth B], G [auth C]	Cisplatin Cl2 H6 N2 Pt LXZZYRPGZAFOLE-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.290 (Depositor), 0.293 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.412	α = 90
b = 34.805	β = 112.28
c = 115.225	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-25 
Deposition Author(s): Bertini, I., Blazevits, O., Calderone, V., Jaifei, M., Vieru, M., Amori, I., Cozzolino, M., Carri, M.T., Banci, L.

Revision History  

• Version 1.0: 2012-04-25
  Type: Initial release
  
• Version 1.1: 2013-07-03
  Changes: Database references
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary