Vesicle-associated membrane protein 2 (VAMP2) is a 116-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P63027.
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The mean pLDDT of this model is 78.3 (confident overall). pLDDT is AlphaFold's per-residue confidence score from 0 to 100. In MolViewer, choose the B-factor color scheme to color the model by pLDDT, because AlphaFold stores it in the B-factor column.
| pLDDT band | Meaning | Share of residues |
|---|---|---|
| Above 90 | Very high: backbone and side chains are usually accurate | 28% |
| 70 to 90 | Confident: backbone generally right | 38% |
| 50 to 70 | Low: treat with caution | 31% |
| Below 50 | Very low: often disordered regions | 3% |
What pLDDT means and how to read it
SNAREs (soluble N-ethylmaleimide-sensitive factor-attachment protein receptors) are essential proteins for intracellular membrane fusion. SNAREs localized on opposing membranes assemble to form a trans-SNARE complex, an extended, parallel four-helix bundle whose assembly releases energy that drives membrane fusion. The core SNARE complex typically consists of four alpha-helical domains, three from target membrane SNAREs (t-SNAREs) and one from a vesicle SNARE (v-SNARE) (PubMed:10036234, PubMed:30929742). VAMP2 is a v-SNARE assembling into a SNARE complex with the t-SNAREs SNAP25 and STX1A to mediate the fusion of synaptic vesicles with the presynaptic plasma membrane in neurotransmitter…
Part of the SNARE core complex containing SNAP25, VAMP2 and STX1A; this complex constitutes the basic catalytic machinery of the complex neurotransmitter release apparatus (By similarity). Recruited to the SNARE complex following binding of the SNARE complex component STX1A to STXBP1 (By similarity). This complex binds to CPLX1. Interacts with POPDC1 and STX4 (By similarity). Interacts with VAPA…
Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane, Cell membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 9CKX | X-ray | 1.98 Å | A/B=95-114 |
| 3FIE | X-ray | 2.1 Å | C/D=22-57 |
| 3FII | X-ray | 2.17 Å | B=27-57 |
| 3RK2 | X-ray | 2.2 Å | A/E=28-60 |
| 3RK3 | X-ray | 3.5 Å | A=28-60 |
| 7UDC | EM | 3.7 Å | C=29-83 |
| 3RL0 | X-ray | 3.8 Å | A/E/I/M/Q/U/Y/c=28-60 |
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