3H2P

Human SOD1 D124V Variant

• PDB DOI: https://doi.org/10.2210/pdb3H2P/pdb

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


• Deposited: 2009-04-14 Released: 2010-05-05 
• Deposition Author(s): Seetharaman, S.V., Winkler, D.D., Taylor, A.B., Cao, X., Whitson, L.J., Doucette, P.A., Valentine, J.S., Carroll, M.C., Culotta, V.C., Hart, P.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.202 
• R-Value Work: 0.152 
• R-Value Observed: 0.155 

Starting Model: experimental

Literature

Structures of Pathogenic SOD1 Mutants H80R and D124V: Disrupted Zinc-binding and Compromised Post-translational Modification by the Copper Chaperone CCS

Seetharaman, S.V., Winkler, D.D., Taylor, A.B., Cao, X., Whitson, L.J., Doucette, P.A., Valentine, J.S., Carroll, M.C., Culotta, V.C., Hart, P.J.

To be published.

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: 32.07 kDa 
• Atom Count: 2,135 
• Modelled Residue Count: 255 
• 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	153	Homo sapiens	Mutation(s): 1  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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	E [auth A], H [auth B]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
ZN	C [auth A], D [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACE	F [auth B]	ACETYL GROUP C2 H4 O IKHGUXGNUITLKF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.202 
• R-Value Work: 0.152 
• R-Value Observed: 0.155 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.919	α = 90
b = 57.972	β = 90
c = 105.021	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-05 
Deposition Author(s): Seetharaman, S.V., Winkler, D.D., Taylor, A.B., Cao, X., Whitson, L.J., Doucette, P.A., Valentine, J.S., Carroll, M.C., Culotta, V.C., Hart, P.J.

Revision History  

• Version 1.0: 2010-05-05
  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