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 3K91|pdb_00003k91

Polysulfane Bridge in Cu-Zn Superoxide Dismutase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.218 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model:experimental
View more details

wwPDB Validation  3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Characterization of a covalent polysulfane bridge in copper-zinc superoxide dismutase .

You, Z.Cao, X.Taylor, A.B.Hart, P.J.Levine, R.L.

(2010) Biochemistry 49: 1191-1198

  • PubMed20052996 Search on PubMedSearch on PubMed Central
  • DOI: https://doi.org/10.1021/bi901844d
  • Primary Citation of Related Structures:  
    3K91

  • PubMed Abstract: 

    In the course of studies on human copper-zinc superoxide dismutase (SOD1), we observed a modified form of the protein whose mass was increased by 158 mass units. The covalent modification was characterized, and we established that it is a novel heptasulfane bridge connecting the two Cys111 residues in the SOD1 homodimer. The heptasulfane bridge was visualized directly in the crystal structure of a recombinant human mutant SOD1, H46R/H48Q, produced in yeast. The modification is reversible, with the bridge being cleaved by thiols, by cyanide, and by unfolding of the protein to expose the polysulfane. The polysulfane bridge can be introduced in vitro by incubation of purified SOD1 with elemental sulfur, even under anaerobic conditions and in the presence of a metal chelator. Because polysulfanes and polysulfides can catalyze the generation of reactive oxygen and sulfur species, the modification may endow SOD1 with a toxic gain of function.


  • Organizational Affiliation
    • Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892, USA.
Biological Assembly 1  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (PS5)


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


Find Similar Assemblies

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

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Macromolecule Content 

  • Total Structure Weight: 31.83 kDa 
  • Atom Count: 2,276 
  • Modeled Residue Count: 276 
  • Deposited Residue Count: 306 
  • Unique protein chains: 1

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]153Homo sapiensMutation(s): 2 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PS5
Query on PS5

Download Ideal Coordinates CCD File 
C [auth A]PENTASULFIDE-SULFUR
S5
FBNHIFPJXGPDIP-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.218 (Depositor), 0.210 (DCC) 
  • R-Value Work: 0.188 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.049α = 90
b = 57.925β = 90
c = 104.988γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-09-06
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-27
    Changes: Structure summary
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RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729.


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