MolNFT v1 · #152730 · protein
Structure of the human GLUN1/GLUN2A NMDA receptor in the GLUTAMATE/GLYCINE-bound state at pH 6.3, class II
6IRG · Glutamate receptor ionotropic, NMDA 1: “Structure of the human GLUN1/GLUN2A NMDA receptor in the GLUTAMATE/GLYCINE-bound state at pH 6.3, class II”. Electron microscopy, 20 pockets (best druggability 0.87). MolNFT v1 #152730 on…
- PDB
- 6IRG
- Type
- protein
- Length
- 3,078 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, NMDA 1; Glutamate receptor ionotropic, NMDA 2A
- UniProt
- Q05586, Q12879
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | Glutamate receptor ionotropic, NMDA 1 | protein | 787 | 38% helix, 18% strand | Q05586 |
| B, D | Glutamate receptor ionotropic, NMDA 2A | protein | 752 | 36% helix, 14% strand | Q12879 |
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 | 923 | 0.87 | 0.88 | 95 | empty |
| 2 | 1050 | 0.86 | 0.87 | 96 | empty |
| 3 | 1198 | 0.85 | 0.85 | 93 | empty |
| 4 | 862 | 0.82 | 0.84 | 66 | empty |
| 5 | 1198 | 0.81 | 0.82 | 138 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3180 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 3164 Ų buried · 24 hydrogen bonds · protein-protein
- C–B · 2400 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 2397 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 108 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6IRG · Structure of the human GluN1/GluN2A NMDA receptor in the glutamate/glycine-bound state at… · the same entry in another collection · chain C against C, 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 C against A, TM-score 0.96
- Q12879 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2A (Q12879) · a predicted model of the same protein · chain B 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 Q05586
- Every structure of UniProt Q12879
- Elsewhere: RCSB PDB 6IRG · PDBe 6IRG · UniProt Q05586 · UniProt Q12879
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