Research workbench
Memantine-bound GluN1a-GluN2B NMDA receptors
Analyse Memantine-bound GluN1a-GluN2B NMDA receptors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SAD
- Type
- protein
- Length
- 3,160 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.96
- Source
- Rattus norvegicus
- Molecule
- Glutamate receptor ionotropic, NMDA 1; Glutamate receptor ionotropic, NMDA 2B
- UniProt
- P35439, Q00960
- Ligands
- 377, NAG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · resolution 3.96 · 2 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor ionotropic, NMDA 1 | protein | 795 | 37% helix, 16% strand | P35439 |
| B, D | Glutamate receptor ionotropic, NMDA 2B | protein | 785 | 38% helix, 16% strand | Q00960 |
Ligands and binding sites
- 377 · Memantine · ligand · chains B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains B, C, D, A
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 | 1115 | 0.89 | 0.90 | 138 | 377 |
| 2 | 1100 | 0.82 | 0.83 | 120 | empty |
| 3 | 280 | 0.82 | 0.92 | 57 | empty |
| 4 | 791 | 0.80 | 0.83 | 110 | empty |
| 5 | 1169 | 0.79 | 0.80 | 136 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2886 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 2716 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 2541 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 2406 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 88 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 15 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 7SAD · Memantine-bound GLUN1A-GLUN2B NMDA receptors · the same entry in another collection · chain A against A, TM-score 1.00
- P35439 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 1 (P35439) · a predicted model of the same protein · chain A against A, TM-score 0.93
- Q00960 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2B (Q00960) · 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 P35439
- Every structure of UniProt Q00960
- Elsewhere: RCSB PDB 7SAD · PDBe 7SAD · UniProt P35439 · UniProt Q00960
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