MolNFT v1 · #119484 · protein
GLUN1B-GLUN2B NMDA receptor structure-class X
5FXJ · Glutamate receptor ionotropic, NMDA 1: “GLUN1B-GLUN2B NMDA receptor structure-class X”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #119484 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5FXJ
- Type
- protein
- Length
- 3,105 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, NMDA 1; Glutamate receptor ionotropic, NMDA 2B
- UniProt
- P35439, Q00960
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 37% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 1 | protein | 787 | 37% helix, 10% strand | P35439 |
| B | Glutamate receptor ionotropic, NMDA 2B | protein | 769 | 38% helix, 10% strand | Q00960 |
| C | Glutamate receptor ionotropic, NMDA 1 | protein | 787 | 38% helix, 10% strand | P35439 |
| D | Glutamate receptor ionotropic, NMDA 2B | protein | 762 | 37% helix, 10% strand | Q00960 |
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 | 944 | 0.86 | 0.87 | 147 | empty |
| 2 | 988 | 0.83 | 0.84 | 127 | empty |
| 3 | 1108 | 0.83 | 0.84 | 178 | empty |
| 4 | 902 | 0.81 | 0.83 | 144 | empty |
| 5 | 624 | 0.80 | 0.86 | 122 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1130 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 1120 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 751 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 718 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 43 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5FXJ · GluN1b-GluN2B NMDA receptor structure-Class X · the same entry in another collection · chain D against D, TM-score 1.00
- Q00960 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2B (Q00960) · a predicted model of the same protein · chain D against A, TM-score 0.91
- 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 Q00960
- Elsewhere: RCSB PDB 5FXJ · PDBe 5FXJ · UniProt P35439 · UniProt Q00960
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