MolNFT v1 · #177637 · protein
Structure of the human GLUN1/GLUN2A NMDA receptor in the cgp- 78608/GLUTAMATE bound state
7EOT · Glutamate receptor ionotropic, NMDA 2A: “Structure of the human GLUN1/GLUN2A NMDA receptor in the cgp- 78608/GLUTAMATE bound state”. Electron microscopy, 2 ligands (J86, NAG), 20 pockets (best druggability 0.88). MolNFT v1 #177637…
- PDB
- 7EOT
- Type
- protein
- Length
- 3,088 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, NMDA 2A; Glutamate receptor ionotropic, NMDA 1
- UniProt
- Q12879, Q05586
- Ligands
- J86, NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 2 distinct chains · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor ionotropic, NMDA 2A | protein | 757 | 35% helix, 14% strand | Q12879 |
| B, D | Glutamate receptor ionotropic, NMDA 1 | protein | 787 | 39% helix, 15% strand | Q05586 |
Ligands and binding sites
- J86 · [(1S)-1-[[7-bromanyl-2,3-bis(oxidanylidene)-1,4-dihydroquinoxalin-5-yl]methylamino]ethyl]phosphonic acid · ligand · 2 copies · chains B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.88 | 0.90 | 108 | empty |
| 2 | 842 | 0.86 | 0.88 | 108 | J86 |
| 3 | 763 | 0.85 | 0.88 | 103 | J86 |
| 4 | 1010 | 0.81 | 0.83 | 82 | empty |
| 5 | 964 | 0.81 | 0.83 | 75 | empty |
Interfaces
5 interfaces between chains.
- A–D · 3561 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 3469 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2413 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2392 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 522 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 16 glycan (disulfide, N-glycosylation).
Compared structures
- 7EOT · Structure of the human GluN1/GluN2A NMDA receptor in the CGP-78608/glutamate bound state · the same entry in another collection · chain A against A, TM-score 1.00
- Q05586 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 1 (Q05586) · a predicted model of the same protein · chain B against A, TM-score 0.95
- Q12879 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2A (Q12879) · a predicted model of the same protein · chain A against A, TM-score 0.92
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q12879
- Every structure of UniProt Q05586
- Elsewhere: RCSB PDB 7EOT · PDBe 7EOT · UniProt Q12879 · UniProt Q05586
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