MolNFT v1 · #157040 · protein
Diheteromeric NMDA receptor GLUN1/GLUN2A in the 'extended-1' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 7.4
6MMM · Glutamate receptor ionotropic, NMDA 1: “Diheteromeric NMDA receptor GLUN1/GLUN2A in the 'extended-1' conformation, in complex with glycine and…”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.88). MolNFT v1…
- PDB
- 6MMM
- Type
- protein
- Length
- 3,100 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 0.88
Structure
electron microscopy · 4 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 1 | protein | 777 | 37% helix, 17% strand | P35439 |
| B | Glutamate receptor ionotropic, NMDA 2A | protein | 774 | 34% helix, 15% strand | Q00959 |
| C | Glutamate receptor ionotropic, NMDA 1 | protein | 783 | 37% helix, 16% strand | P35439 |
| D | Glutamate receptor ionotropic, NMDA 2A | protein | 766 | 36% helix, 15% strand | Q00959 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 40 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 | 950 | 0.88 | 0.89 | 107 | empty |
| 2 | 1077 | 0.88 | 0.89 | 164 | empty |
| 3 | 514 | 0.83 | 0.89 | 63 | empty |
| 4 | 1136 | 0.83 | 0.84 | 134 | empty |
| 5 | 708 | 0.83 | 0.86 | 104 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3586 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 3574 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 2722 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 2467 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 34 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 glycan, 8 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 6MMM · Diheteromeric NMDA receptor GluN1/GluN2A in the 'Extended-1' conformation, in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q00959 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2A (Q00959) · a predicted model of the same protein · chain B against A, TM-score 0.86
- 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 0.84
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 6MMM · PDBe 6MMM · UniProt P35439 · UniProt Q00959
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