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 7.4
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
- 6MMK
- Type
- protein
- Length
- 3,122 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 6.08
- Source
- Rattus norvegicus
- 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 · resolution 6.08 · 4 distinct chains · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 1 | protein | 782 | 38% helix, 17% strand | P35439 |
| B | Glutamate receptor ionotropic, NMDA 2A | protein | 772 | 34% helix, 15% strand | Q00959 |
| C | Glutamate receptor ionotropic, NMDA 1 | protein | 790 | 38% helix, 15% strand | P35439 |
| D | Glutamate receptor ionotropic, NMDA 2A | protein | 778 | 34% helix, 14% strand | Q00959 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 40 copies · chains A, C, D, B
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 | 968 | 0.89 | 0.90 | 102 | empty |
| 2 | 1030 | 0.84 | 0.85 | 116 | empty |
| 3 | 636 | 0.81 | 0.86 | 86 | empty |
| 4 | 927 | 0.80 | 0.82 | 115 | empty |
| 5 | 429 | 0.80 | 0.88 | 58 | empty |
Interfaces
5 interfaces between chains.
- C–D · 4242 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 3908 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 2866 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 2707 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 148 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 34 glycan, 9 disulfide (N-glycosylation, disulfide).
Compared structures
- 6MMK · 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 0.92
- 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 6MMK · PDBe 6MMK · UniProt P35439 · UniProt Q00959
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.