Research workbench
GLUN1B-GLUN2B NMDA receptor structure-class Y
Analyse GLUN1B-GLUN2B NMDA receptor structure-class Y in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FXK
- Type
- protein
- Length
- 3,118 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-methyl-D-aspartate receptor GLUN1; N-methyl-D-aspartate receptor GLUN2B
- UniProt
- P35439, Q00960
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 38% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-methyl-D-aspartate receptor GLUN1 | protein | 793 | 39% helix, 13% strand | P35439 |
| B | N-methyl-D-aspartate receptor GLUN2B | protein | 767 | 38% helix, 14% strand | Q00960 |
| C | N-methyl-D-aspartate receptor GLUN1 | protein | 792 | 39% helix, 13% strand | P35439 |
| D | N-methyl-D-aspartate receptor GLUN2B | protein | 766 | 38% helix, 14% 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 | 839 | 0.85 | 0.88 | 149 | empty |
| 2 | 906 | 0.82 | 0.84 | 145 | empty |
| 3 | 601 | 0.81 | 0.87 | 102 | empty |
| 4 | 526 | 0.80 | 0.86 | 98 | empty |
| 5 | 688 | 0.79 | 0.84 | 101 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1279 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 1271 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 865 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 855 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5FXK · GluN1b-GluN2B NMDA receptor structure-Class Y · 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 B 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 0.90
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 5FXK · PDBe 5FXK · UniProt P35439 · UniProt Q00960
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