Glutamate receptor ionotropic, NMDA 2A (Grin2a) is a 1464-residue protein from Rattus norvegicus. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q00959.
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The mean pLDDT of this model is 60.8 (low 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 | 18% |
| 70 to 90 | Confident: backbone generally right | 30% |
| 50 to 70 | Low: treat with caution | 9% |
| Below 50 | Very low: often disordered regions | 43% |
What pLDDT means and how to read it
Component of N-methyl-D-aspartate (NMDA) receptors (NMDARs) that function as heterotetrameric, ligand-gated cation channels with high calcium permeability and voltage-dependent block by Mg(2+) (Probable) (PubMed:11160393, PubMed:11929923, PubMed:1350383, PubMed:14602821, PubMed:30500536). NMDARs participate in synaptic plasticity for learning and memory formation by contributing to the slow phase of excitatory postsynaptic current, long-term synaptic potentiation, and learning (By similarity). Channel activation requires binding of the neurotransmitter L-glutamate to the GluN2 subunit, glycine or D-serine binding to the GluN1 subunit, plus membrane depolarization to eliminate channel…
Heterotetramer. Forms heterotetrameric channels composed of two GluN1/zeta subunits (GRIN1), and two identical GluN2/epsilon subunits (GRIN2A, GRIN2B, GRIN2C or GRIN2D) or GluN3 subunits (GRIN3A or GRIN3B) (in vitro) (PubMed:1350383, PubMed:8428958, PubMed:28384476, PubMed:16281028, PubMed:23625947, PubMed:24462099, PubMed:27618671, PubMed:27916457, PubMed:28468946, PubMed:28760974, Ref.29). Can…
Cell projection, dendritic spine, Cell membrane, Synapse, Postsynaptic cell membrane, Cytoplasmic vesicle membrane, Postsynaptic density membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 4JWX | X-ray | 1.5 Å | A=404-801 |
| 5U8C | X-ray | 1.6 Å | B=402-802 |
| 9GJ1 | X-ray | 1.62 Å | A=401-539, A=661-802 |
| 6UZ6 | X-ray | 1.66 Å | B=402-539, B=661-800 |
| 2A5S | X-ray | 1.7 Å | A=401-802 |
| 5I57 | X-ray | 1.7 Å | B=402-539, B=661-800 |
| 9NYZ | X-ray | 1.71 Å | B=402-539, B=661-802 |
| 4NF8 | X-ray | 1.86 Å | B=402-802 |
| 6UZR | X-ray | 1.87 Å | B=402-539, B=661-802 |
| 4NF5 | X-ray | 1.9 Å | B=402-802 |
| 6UZG | X-ray | 1.94 Å | B=402-539, B=661-802 |
| 5VII | X-ray | 1.95 Å | B=402-539, B=661-802 |
| 9GIB | X-ray | 1.95 Å | A=401-539, A=661-802 |
| 2A5T | X-ray | 2.0 Å | B=401-802 |
| 4NF4 | X-ray | 2.0 Å | B=402-802 |
| 6OVE | X-ray | 2.0 Å | B=402-539, B=568-801 |
| 9DA9 | X-ray | 2.05 Å | B=402-802 |
| 6USU | X-ray | 2.09 Å | B=402-539, B=661-802 |
| 9GIG | X-ray | 2.09 Å | A=401-539, A=661-802 |
| 4NF6 | X-ray | 2.1 Å | B=402-802 |
Showing 20 of 65 experimental structures (best resolution first).
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