MolNFT v1 · #157049 · protein
Triheteromeric NMDA receptor GLUN1/GLUN2A/GLUN2A* extracellular domain in the '2-knuckle-asymmetric' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 7.4
6MMV · Glutamate receptor ionotropic, NMDA 1: “Triheteromeric NMDA receptor GLUN1/GLUN2A/GLUN2A* extracellular domain in the '2-knuckle-asymmetric'…”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 6MMV
- Type
- protein
- Length
- 2,598 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 0.83
Structure
electron microscopy · 4 distinct chains · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 1 | protein | 658 | 33% helix, 20% strand | P35439 |
| B | Glutamate receptor ionotropic, NMDA 2A | protein | 642 | 29% helix, 19% strand | Q00959 |
| C | Glutamate receptor ionotropic, NMDA 1 | protein | 656 | 32% helix, 22% strand | P35439 |
| D | Glutamate receptor ionotropic, NMDA 2A | protein | 642 | 29% helix, 19% strand | Q00959 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 38 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 | 929 | 0.83 | 0.85 | 122 | empty |
| 2 | 1012 | 0.83 | 0.84 | 117 | empty |
| 3 | 971 | 0.77 | 0.79 | 110 | empty |
| 4 | 891 | 0.77 | 0.80 | 77 | empty |
| 5 | 340 | 0.75 | 0.86 | 42 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2384 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2089 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1333 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1316 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 410 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 6MMV · Triheteromeric NMDA receptor GluN1/GluN2A/GluN2A* Extracellular Domain in the… · 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 0.97
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 6MMV · PDBe 6MMV · UniProt P35439 · UniProt Q00959
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