Glutamate receptor ionotropic, NMDA 1 (Grin1) is a 938-residue protein from Rattus norvegicus. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P35439.
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The mean pLDDT of this model is 82.8 (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 | 55% |
| 70 to 90 | Confident: backbone generally right | 28% |
| 50 to 70 | Low: treat with caution | 7% |
| Below 50 | Very low: often disordered regions | 10% |
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+) (PubMed:1350383, PubMed:1388270, PubMed:1834949, PubMed:8428958). NMDARs participate in synaptic plasticity for learning and memory formation by contributing to the long-term potentiation (LTP) (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 inhibition by Mg(2+) (PubMed:11823786, PubMed:1350383, PubMed:1388270, PubMed:15996549,…
Heterotetramer; the NMDAR subunits are modular and harbor tiered domains that function in concert to regulate opening and closing of the cation-selective ion channel pore (PubMed:15996549, PubMed:16281028, PubMed:18177891, PubMed:21389213, PubMed:24876489, PubMed:27135925, PubMed:28384476, PubMed:28468946, Ref.36). Forms heterotetrameric channels composed of two GluN1/zeta subunits (GRIN1), and…
Cell membrane, Postsynaptic cell membrane, Synaptic cell membrane, Postsynaptic density membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 1PB7 | X-ray | 1.35 Å | A=394-800 |
| 1Y20 | X-ray | 1.4 Å | A=394-544, A=663-800 |
| 1PB8 | X-ray | 1.45 Å | A=394-800 |
| 1Y1Z | X-ray | 1.5 Å | A=394-544, A=663-800 |
| 1PB9 | X-ray | 1.6 Å | A=394-800 |
| 5U8C | X-ray | 1.6 Å | A=394-544, A=663-800 |
| 6UZ6 | X-ray | 1.66 Å | A=394-544, A=663-800 |
| 5I57 | X-ray | 1.7 Å | A=394-544, A=663-800 |
| 9NYZ | X-ray | 1.71 Å | A=394-544, A=663-800 |
| 1Y1M | X-ray | 1.8 Å | A/B=394-544, A/B=663-800 |
| 4NF8 | X-ray | 1.86 Å | A=394-544, A=663-800 |
| 6UZR | X-ray | 1.87 Å | A=394-544, A=663-800 |
| 4KCC | X-ray | 1.89 Å | A=394-544, A=663-800 |
| 1PBQ | X-ray | 1.9 Å | A/B=394-800 |
| 4NF5 | X-ray | 1.9 Å | A=394-544, A=663-800 |
| 6UZG | X-ray | 1.94 Å | A=394-544, A=663-800 |
| 5VII | X-ray | 1.95 Å | A=394-544, A=663-800 |
| 2A5T | X-ray | 2.0 Å | A=394-800 |
| 4NF4 | X-ray | 2.0 Å | A=394-544, A=663-800 |
| 6OVE | X-ray | 2.0 Å | A=394-544, A=663-800 |
Showing 20 of 119 experimental structures (best resolution first).
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