01/3D Structure
? About the 3D Viewer
Mol* (pronounced "molstar") is an open-source molecular visualization tool used by the Protein Data Bank and AlphaFold Database. Learn more at molstar.org.
Controls:
- Rotate: Click and drag
- Zoom: Scroll wheel or pinch
- Pan: Right-click and drag (or two-finger drag)
- Reset: Double-click to reset view
What am I looking at?
This is a predicted 3D structure of the protein. The ribbon diagram shows the protein backbone—helices appear as coils, sheets as arrows, and loops as simple lines. The shape determines how the protein functions: where it binds to other molecules, how it catalyzes reactions, and how mutations might disrupt its activity.
Color legend:
The structure is colored by pLDDT confidence score, which indicates how confident AlphaFold is in each region's predicted position:
- Blue (>90): Very high confidence
- Cyan (70-90): Confident
- Yellow (50-70): Low confidence
- Orange (<50): Very low confidence, likely disordered
02/AI Analysis
TLDR
SOD1 (superoxide dismutase 1) is an enzyme that protects cells from oxidative damage, and mutations in this protein cause about 20% of familial ALS cases. The A4V mutation, located at position 4 near the protein's N-terminus, is one of the most common and aggressive SOD1 mutations in North American ALS patients. AlphaFold2 predicted the A4V structure with very high confidence (average 97.8), providing a reliable structural model to understand how this mutation may destabilize the protein and contribute to the toxic aggregation seen in ALS.
Detailed Analysis
Works Cited
Similar Research
03/Research Data
ClinVar Classification
Review: criteria provided, multiple submitters
Last evaluated: 2026-01-01
Population Frequency
No population data available
Disease Associations
1766 totalShowing 5 of 1766 associations
AI Research Brief
Research brief will be generated when agent findings are available.
04/AlphaFold Metrics
05/Domain Annotations
Functional Sites
Binding Partners
Gene Ontology
06/Structural Caption
SOD1 A4V variant shows highly confident fold (pLDDT 97.8) with no apparent structural destabilization despite its association with familial ALS.
The SOD1 A4V structure shows exceptional confidence with an average pLDDT of 97.8 and 100% of residues (154/154) in the high-confidence range. No destabilized regions are observed.
Without specific domain annotations, the uniformly high confidence across all 154 residues suggests a compact, well-folded β-barrel structure typical of superoxide dismutase enzymes.
The A4V mutation, a common ALS-associated variant, does not destabilize the overall fold in this model, though it may affect local dynamics, metal binding, or protein aggregation propensity not captured by static structure prediction.
07/Peptide Therapeutics
Aggregation Analysis
Aggregation propensity analysis identifies 1 hotspots (average score: 0.01) using Pawar+KyteDoolittle+charge algorithm.
08/Known Inhibitors
Known Binders from ChEMBL
09/Candidate Peptides
De Novo Peptide Design Pipeline
Pipeline: BoltzGen (de novo binder design) → Boltz-2 rescore → 8-gate wetlab filter → PK + BBB advisory gates. Target site selected from UniProt curated annotations, P2Rank pocket prediction, and aggregation propensity (in that priority order). Advisory gates annotate each candidate with estimated serum half-life, renal/immunogenicity risk, and (for CNS targets) a recommended blood-brain-barrier shuttle conjugation — without silently dropping designs.
Loading candidate statistics...
Sequences are withheld pending IP review. Full candidate data (sequences,
scores, CIF files) is available to authorized reviewers via the
/api/private/candidates/{fold_id} endpoint with
X-Private-Key.
Legacy candidates (charge-complementary)
Target Region
Residues 149–153 (0.58 aggregation score)Candidate ID
CP-SOD1-001
(7 residues · computational design)
10/Agent Findings
Literature Agent (1)
These papers provide crucial insights into SOD1-A4V ALS management, including the first targeted gene therapy (Tofersen), structural mechanisms of SOD1 protein aggregation, and presymptomatic biomarkers for early detection. The research establishes both therapeutic approaches and molecular understanding directly applicable to SOD1-A4V patients.
Clinical Agent (1)
The first baseline data collection for SOD1 A4V represents the initial establishment of reference parameters for this highly aggressive ALS variant, which typically causes symptom onset within 1-2 years and rapid disease progression. This baseline is clinically critical because A4V patients have an extremely short survival time (often 6-18 months from symptom onset), making early and accurate biomarker establishment essential for monitoring disease trajectory and evaluating therapeutic interventions. These initial measurements will serve as the foundation for tracking the accelerated motor neuron degeneration characteristic of this variant and may inform urgent treatment decisions given the compressed clinical timeline.
Structural Agent (1)
AlphaFold structure update: Baseline check: 1 structure(s) found
Supplements Agent (1)
The therapeutic landscape for SOD1 A4V-related ALS shows limited supplement and peptide options currently in clinical testing. Most relevant trials focus on peptide-based therapeutics like RAG-17 and nucleic acid approaches like ALN-SOD targeting SOD1 expression. Natural product screening and small molecule inhibitors targeting SOD1 trimers represent emerging supplement-related approaches in preclinical development.
Synthesis Agent (1)
Synthesis of 5 findings (clinical, literature, peptides, structural, supplements): The SOD1 A4V variant represents one of the most aggressive forms of familial ALS, with recent resear...
Peptide Agent (1)
SOD1 A4V: 10 known binders (top: 67.0 nM); 1 candidate peptides designed