PDBsum entry 3t5w

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
Protein chain
(+ 6 more) 153 a.a.
SO4 ×12
CU1 ×12
_ZN ×12
Waters ×1746
PDB id:
Name: Oxidoreductase
Title: 2me modified human sod1
Structure: Superoxide dismutase [cu-zn]. Chain: a, b, d, e, f, g, h, i, j, k, l, m. Synonym: copper zinc superoxide dismutase, superoxide dismu hsod1. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: sod1. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.80Å     R-factor:   0.202     R-free:   0.241
Authors: K.Ihara,Y.Yamaguchi,H.Torigoe,S.Wakatsuki,N.Taniguchi,K.Suzu N.Fujiwara
Key ref: K.Ihara et al. (2012). Structural switching of Cu,Zn-superoxide dismutases at loop VI: insights from the crystal structure of 2-mercaptoethanol-modified enzyme. Biosci Rep, 32, 539-548. PubMed id: 22804629
28-Jul-11     Release date:   01-Aug-12    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P00441  (SODC_HUMAN) -  Superoxide dismutase [Cu-Zn]
154 a.a.
153 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Superoxide dismutase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 superoxide + 2 H+ = O2 + H2O2
2 × superoxide
+ 2 × H(+)
= O(2)
+ H(2)O(2)
      Cofactor: Iron or manganese or (zinc and copper)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   17 terms 
  Biological process     reactive oxygen species metabolic process   60 terms 
  Biochemical function     antioxidant activity     12 terms  


    Added reference    
Biosci Rep 32:539-548 (2012)
PubMed id: 22804629  
Structural switching of Cu,Zn-superoxide dismutases at loop VI: insights from the crystal structure of 2-mercaptoethanol-modified enzyme.
K.Ihara, N.Fujiwara, Y.Yamaguchi, H.Torigoe, S.Wakatsuki, N.Taniguchi, K.Suzuki.
Cu,Zn SOD1 (superoxide dismutase 1) is implicated in FALS (familial amyotrophic lateral sclerosis) through the accumulation of misfolded proteins that are toxic to neuronal cells. Loop VI (residues 102-115) of the protein is at the dimer interface and could play a critical role in stability. The free cysteine residue, Cys111 in the loop, is readily oxidized and alkylated. We have found that modification of this Cys111 with 2-ME (2-mercaptoethanol; 2-ME-SOD1) stabilizes the protein and the mechanism may provide insights into destabilization and the formation of aggregated proteins. Here, we determined the crystal structure of 2-ME-SOD1 and find that the 2-ME moieties in both subunits interact asymmetrically at the dimer interface and that there is an asymmetric configuration of segment Gly108 to Cys111 in loop VI. One loop VI of the dimer forms a 310-helix (Gly108 to His110) within a unique β-bridge stabilized by a hydrogen bond between Ser105-NH and His110-CO, while the other forms a β-turn without the H-bond. The H-bond (H-type) and H-bond free (F-type) configurations are also seen in some wild-type and mutant human SOD1s in the Protein Data Bank suggesting that they are interconvertible and an intrinsic property of SOD1s. The two structures serve as a basis for classification of these proteins and hopefully a guide to their stability and role in pathophysiology.