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: 1.9 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1002/1873-3468.13055
  • Primary Citation of Related Structures:  

  • 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 structure ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Superoxide dismutase [Cu-Zn]
A, B, C, D, E, F, G, H, I, J
180Homo sapiensMutation(s): 0 
Gene Names: SOD1
EC: 1.15.1.1
Find proteins for P00441 (Homo sapiens)
Go to Gene View: SOD1
Go to UniProtKB:  P00441
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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Download CCD File 
A, B, C, D, E, F, G, H, I
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PS5
Query on PS5

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Download CCD File 
B, C, E
PENTASULFIDE-SULFUR
S5
FBNHIFPJXGPDIP-UHFFFAOYSA-L
 Ligand Interaction
946
Query on 946

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Download CCD File 
B, D, H
4-[(1~{R})-2-(naphthalen-2-ylmethylamino)-1-oxidanyl-ethyl]benzene-1,2-diol
(1-(3,4-dihydroxyphenyl)-2-((naphthalen-1-ylmethyl)amino)ethan-1-one
C19 H19 N O3
KSDGEFPHPRYPCZ-IBGZPJMESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
946Kd: 33000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.179 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 243.941α = 90.00
b = 243.941β = 90.00
c = 144.775γ = 120.00
Software Package:
Software NamePurpose
HKL-3000data reduction
MOLREPphasing
REFMACrefinement
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-11-21
    Type: Initial release