Research workbench
Structure of the human GLUN1/GLUN2A NMDA receptor in the GLUTAMATE/GLYCINE-bound state at pH 7.8
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
- 6IRA
- Type
- protein
- Length
- 3,080 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
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, B | Glutamate receptor ionotropic, NMDA 2A | protein | 751 | 37% helix, 16% strand | Q12879 |
| A, C | Glutamate receptor ionotropic, NMDA 1 | protein | 789 | 38% helix, 17% strand | Q05586 |
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 | 1038 | 0.85 | 0.86 | 137 | empty |
| 2 | 1084 | 0.84 | 0.85 | 131 | empty |
| 3 | 610 | 0.84 | 0.88 | 66 | empty |
| 4 | 1102 | 0.83 | 0.84 | 135 | empty |
| 5 | 752 | 0.79 | 0.83 | 72 | empty |
Interfaces
5 interfaces between chains.
- D–C · 3416 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 3357 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 2713 Ų buried · 14 hydrogen bonds · protein-protein
- D–A · 2695 Ų buried · 11 hydrogen bonds · protein-protein
- D–B · 273 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6IRA · Structure of the human GluN1/GluN2A NMDA receptor in the glutamate/glycine-bound state at… · the same entry in another collection · chain D against D, 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 A against A, TM-score 0.97
- Q12879 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2A (Q12879) · a predicted model of the same protein · chain D against A, TM-score 0.91
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 6IRA · PDBe 6IRA · UniProt Q12879 · UniProt Q05586
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