2WYZ

L38V SOD1 mutant complexed with UMP

• PDB DOI: https://doi.org/10.2210/pdb2WYZ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): Yes 


• Deposited: 2009-11-20 Released: 2010-10-27 
• Deposition Author(s): Antonyuk, S.V., Strange, R.W., Hasnain, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.239 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 

Starting Model: experimental

Literature

Structural Discovery of Small Molecule Binding Sites in Cu-Zn Human Superoxide Dismutase Familial Amyotrophic Lateral Sclerosis Mutants Provides Insights for Lead Optimization.

Antonyuk, S.V., Strange, R.W., Hasnain, S.S.

(2010) J Med Chem 53: 1402

• PubMed: 20067275 
• DOI: https://doi.org/10.1021/jm9017948
• Primary Citation of Related Structures:  
  2WYT, 2WYZ, 2WZ0, 2WZ5, 2WZ6


• PubMed Abstract: 
  

  Dominant inheritance of point mutations in CuZn superoxide dismutase (SOD1) is the best characterized subset of familial amyotrophic lateral sclerosis (FALS) and accounts for some 20% of the known familial cases. We report the discovery and visualization via cocrystallography of two ligand-binding pockets in human SOD1 and its pathogenic mutants that have opened up the real possibility of undertaking lead compound discovery using a fragment-based approach for therapeutic purposes for SOD1 associated motor neuron disease.

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Organizational Affiliation: 

Molecular Biophysics Group, School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 32.76 kDa 
• Atom Count: 2,726 
• Modelled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SUPEROXIDE DISMUTASE [CU-ZN]	A, B [auth F]	153	Homo sapiens	Mutation(s): 1  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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U5P	G [auth A]	URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N
SO4	F [auth A], K [auth F], L [auth F], M [auth F]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A], E [auth A], I [auth F], J [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU	D [auth A], H [auth F]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A, B [auth F]	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.239 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.717	α = 90
b = 67.589	β = 105.98
c = 50.777	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-27 
Deposition Author(s): Antonyuk, S.V., Strange, R.W., Hasnain, S.S.

Revision History  

• Version 1.0: 2010-10-27
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-07-12
  Changes: Derived calculations
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.5: 2024-11-13
  Changes: Structure summary