Research workbench
Diheteromeric NMDA receptor GLUN1/GLUN2A in the '1-knuckle' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 6.1
Analyse Diheteromeric NMDA receptor GLUN1/GLUN2A in the '1-knuckle' conformation, in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MM9
- Type
- protein
- Length
- 3,126 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 · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 1 | protein | 784 | 38% helix, 18% strand | P35439 |
| B | Glutamate receptor ionotropic, NMDA 2A | protein | 772 | 34% helix, 15% strand | Q00959 |
| C | Glutamate receptor ionotropic, NMDA 1 | protein | 790 | 37% helix, 17% strand | P35439 |
| D | Glutamate receptor ionotropic, NMDA 2A | protein | 780 | 35% helix, 16% strand | Q00959 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 34 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 | 1068 | 0.89 | 0.90 | 125 | empty |
| 2 | 395 | 0.82 | 0.90 | 52 | empty |
| 3 | 464 | 0.82 | 0.89 | 61 | empty |
| 4 | 1122 | 0.80 | 0.82 | 111 | empty |
| 5 | 933 | 0.80 | 0.82 | 100 | empty |
Interfaces
5 interfaces between chains.
- C–D · 4265 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 3813 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 2850 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 2833 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 176 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 35 glycan, 9 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 6MM9 · Diheteromeric NMDA receptor GluN1/GluN2A in the '1-Knuckle' conformation, in complex with… · the same entry in another collection · chain D against D, 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 0.93
- P35439 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 1 (P35439) · a predicted model of the same protein · chain C 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 Q00959
- Elsewhere: RCSB PDB 6MM9 · PDBe 6MM9 · UniProt P35439 · UniProt Q00959
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