MolNFT v1 · #177798 · protein
Structure of the human GLUN1-GLUN2A NMDA receptor in complex with S- ketamine, glycine and glutamate
7EU7 · Glutamate receptor ionotropic, NMDA 1: “Structure of the human GLUN1-GLUN2A NMDA receptor in complex with S- ketamine, glycine and glutamate”. Electron microscopy, 4 ligands (GLY, GLU, JC9), 20 pockets (best druggability 0.82).…
- PDB
- 7EU7
- Type
- protein
- Length
- 3,130 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
- Ligands
- GLY, GLU, JC9, NAG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor ionotropic, NMDA 1 | protein | 784 | 38% helix, 16% strand | Q05586 |
| B, D | Glutamate receptor ionotropic, NMDA 2A | protein | 781 | 37% helix, 15% strand | Q12879 |
Ligands and binding sites
- GLY · Glycine · ligand · 2 copies · chains A, C
- GLU · Glutamic acid · ligand · 2 copies · chains B, D
- JC9 · (2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one · ligand · chains A, B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 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 | 639 | 0.82 | 0.87 | 78 | JC9 |
| 2 | 694 | 0.81 | 0.85 | 108 | empty |
| 3 | 1007 | 0.77 | 0.79 | 92 | empty |
| 4 | 1184 | 0.77 | 0.79 | 88 | empty |
| 5 | 217 | 0.75 | 0.90 | 40 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2438 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 2103 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 1885 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 1767 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 371 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 glycan, 16 disulfide (N-glycosylation, disulfide).
Compared structures
- 7EU7 · Structure of the human GluN1-GluN2A NMDA receptor in complex with S-ketamine, glycine and… · 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 0.97
- 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 0.91
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 Q05586
- Every structure of UniProt Q12879
- Elsewhere: RCSB PDB 7EU7 · PDBe 7EU7 · UniProt Q05586 · UniProt Q12879
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