5YUL | pdb_00005yul

Native Structure of hSOD1 in P6322 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.227 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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 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.

Macromolecule Content 

  • Total Structure Weight: 160.79 kDa 
  • Atom Count: 12,502 
  • Modeled Residue Count: 1,511 
  • Deposited Residue Count: 1,540 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]154Homo sapiensMutation(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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00441
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S4P
(Subject of Investigation/LOI)

Query on S4P



Download:Ideal Coordinates CCD File
L [auth A],
P [auth C],
S [auth D],
X [auth J]
Dihydrogen tetrasulfide
H2 S4
IKRMQEUTISXXQP-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
Q [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
K [auth A]
M [auth H]
N [auth B]
O [auth C]
R [auth D]
K [auth A],
M [auth H],
N [auth B],
O [auth C],
R [auth D],
T [auth E],
U [auth F],
V [auth G],
W [auth I]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.227 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 242.634α = 90
b = 242.634β = 90
c = 144.113γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



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, Derived calculations, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Structure summary