Research workbench
Diheteromeric NMDA receptor GLUN1/GLUN2A in the 'splayed-open' conformation, in complex with glycine and glutamate, in the presence of 1 millimolar zinc chloride, and at pH 7.4
Analyse Diheteromeric NMDA receptor GLUN1/GLUN2A in the 'splayed-open' conformation, in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MMI
- Type
- protein
- Length
- 3,079 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
- P35439, Q00959
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 4 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 1 | protein | 784 | 38% helix, 16% strand | P35439 |
| B | Glutamate receptor ionotropic, NMDA 2A | protein | 760 | 36% helix, 15% strand | Q00959 |
| C | Glutamate receptor ionotropic, NMDA 1 | protein | 775 | 38% helix, 17% strand | P35439 |
| D | Glutamate receptor ionotropic, NMDA 2A | protein | 760 | 35% helix, 17% strand | Q00959 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 47 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 | 999 | 0.89 | 0.91 | 115 | empty |
| 2 | 1011 | 0.84 | 0.85 | 120 | empty |
| 3 | 552 | 0.83 | 0.88 | 75 | empty |
| 4 | 376 | 0.82 | 0.91 | 71 | empty |
| 5 | 816 | 0.82 | 0.84 | 83 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3689 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 3105 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 2186 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1932 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 265 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 glycan, 9 disulfide (N-glycosylation, disulfide).
Compared structures
- 6MMI · Diheteromeric NMDA receptor GluN1/GluN2A in the 'Splayed-Open' conformation, in complex… · the same entry in another collection · chain C against C, 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 0.75
- Q00959 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2A (Q00959) · a predicted model of the same protein · chain D against A, TM-score 0.69
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 Q00959
- Elsewhere: RCSB PDB 6MMI · PDBe 6MMI · UniProt P35439 · UniProt Q00959
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