Research workbench
Structure of the human GLUN1/GLUN2A NMDA receptor in the GLYCINE/GLUTAMATE/GNE-6901/9-aa bound state
Analyse Structure of the human GLUN1/GLUN2A NMDA receptor in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EOU
- Type
- protein
- Length
- 3,084 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
- 6RM, AA, NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor ionotropic, NMDA 2A | protein | 759 | 39% helix, 13% strand | Q12879 |
| B, D | Glutamate receptor ionotropic, NMDA 1 | protein | 783 | 39% helix, 15% strand | Q05586 |
Ligands and binding sites
- 6RM · 7-[(4-fluoranylphenoxy)methyl]-3-[(1~{R},2~{R})-2-(hydroxymethyl)cyclopropyl]-2-methyl-[1,3]thiazolo[3, 2-a]pyrimidin-5-one · ligand · 2 copies · chains A, B, C, D
- AA · 9-aminoacridine · ligand
- 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 | 680 | 0.86 | 0.89 | 89 | empty |
| 2 | 971 | 0.83 | 0.84 | 95 | empty |
| 3 | 882 | 0.83 | 0.84 | 108 | 6RM |
| 4 | 838 | 0.82 | 0.84 | 86 | empty |
| 5 | 133 | 0.80 | 0.97 | 33 | empty |
Interfaces
5 interfaces between chains.
- A–D · 3419 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 3391 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2295 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 2278 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 517 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 16 glycan (disulfide, N-glycosylation).
Compared structures
- 7EOU · Structure of the human GluN1/GluN2A NMDA receptor in the glycine/glutamate/GNE-6901/9-AA… · 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 0.88
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 7EOU · PDBe 7EOU · UniProt Q12879 · UniProt Q05586
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