MolNFT v1 · #157047 · protein
Triheteromeric NMDA receptor GLUN1/GLUN2A/GLUN2A* in the '1-knuckle' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 7.4
6MMT · Glutamate receptor ionotropic, NMDA 1: “Triheteromeric NMDA receptor GLUN1/GLUN2A/GLUN2A* in the '1-knuckle' conformation, in complex with glycine…”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT…
- PDB
- 6MMT
- Type
- protein
- Length
- 3,110 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 0.87
Structure
electron microscopy · 4 distinct chains · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 1 | protein | 782 | 37% helix, 16% strand | P35439 |
| B | Glutamate receptor ionotropic, NMDA 2A | protein | 772 | 34% helix, 15% strand | Q00959 |
| C | Glutamate receptor ionotropic, NMDA 1 | protein | 786 | 37% helix, 16% strand | P35439 |
| D | Glutamate receptor ionotropic, NMDA 2A | protein | 770 | 34% helix, 15% strand | Q00959 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 37 copies · chains A, C, B, 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 | 826 | 0.87 | 0.90 | 136 | empty |
| 2 | 956 | 0.85 | 0.87 | 127 | empty |
| 3 | 417 | 0.83 | 0.90 | 54 | empty |
| 4 | 1033 | 0.83 | 0.83 | 120 | empty |
| 5 | 524 | 0.81 | 0.87 | 67 | empty |
Interfaces
5 interfaces between chains.
- C–D · 3937 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 3810 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 2658 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 2639 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 262 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 glycan, 9 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 6MMT · Triheteromeric NMDA receptor GluN1/GluN2A/GluN2A* in the '1-Knuckle' conformation, in… · 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 D against A, TM-score 0.94
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 6MMT · PDBe 6MMT · UniProt P35439 · UniProt Q00959
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