5YTO

Crystal Structure of human Superoxide Dismutase I (hSOD1) in complex with a napthalene-catechol linked compound.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Assessment of ligand binding at a site relevant to SOD1 oxidation and aggregation

Manjula, R.Wright, G.S.A.Strange, R.W.Padmanabhan, B.

(2018) FEBS Lett 592: 1725-1737

  • DOI: https://doi.org/10.1002/1873-3468.13055
  • Primary Citation of Related Structures:  
    5YTO, 5YTU, 5YUL

  • PubMed Abstract: 

    Cu/Zn superoxide dismutase-1 (SOD1) mutations are causative for a subset of amyotrophic lateral sclerosis (ALS) cases. These mutations lead to structural instability, aggregation and ultimately motor neuron death. We have determined crystal structures of SOD1 in complex with a naphthalene-catechol-linked compound which binds with low micro-molar affinity to a site important for oxidative damage-induced aggregation. SOD1 Trp32 oxidation is indeed significantly inhibited by ligand binding. Our work shows how compound linking can be applied successfully to ligand interactions on the SOD1 surface to generate relatively good binding strength. The ligand, positioned in a region important for SOD1 fibrillation, offers the possibility that it, or a similar compound, could prevent the abnormal self-association that drives SOD1 toxicity in ALS.


  • Organizational Affiliation

    Department of Biophysics, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
180Homo 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
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
946 (Subject of Investigation/LOI)
Query on 946

Download Ideal Coordinates CCD File 
AA [auth H],
O [auth B],
U [auth D]
4-[(1~{R})-2-(naphthalen-2-ylmethylamino)-1-oxidanyl-ethyl]benzene-1,2-diol
C19 H19 N O3
KSDGEFPHPRYPCZ-IBGZPJMESA-N
PS5
Query on PS5

Download Ideal Coordinates CCD File 
P [auth B],
S [auth C],
W [auth E]
PENTASULFIDE-SULFUR
S5
FBNHIFPJXGPDIP-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
L [auth A],
N [auth B],
R [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth I]
K [auth A]
M [auth B]
Q [auth C]
T [auth D]
BA [auth I],
K [auth A],
M [auth B],
Q [auth C],
T [auth D],
V [auth E],
X [auth F],
Y [auth G],
Z [auth H]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 243.941α = 90
b = 243.941β = 90
c = 144.775γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-20
    Changes: Structure summary