Research workbench
Crystal structure of the AMPA receptor GLUA2/A3 N-terminal domain heterodimer
Analyse Crystal structure of the AMPA receptor GLUA2/A3 N-terminal domain heterodimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FWY
- Type
- protein
- Length
- 1,494 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2; Glutamate receptor 3
- UniProt
- P19491, P19492
- Ligands
- NAG, SO4
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor 2 | protein | 371 | 37% helix, 24% strand | P19491 |
| B | Glutamate receptor 3 | protein | 379 | 37% helix, 21% strand | P19492 |
| C | Glutamate receptor 2 | protein | 367 | 38% helix, 25% strand | P19491 |
| D | Glutamate receptor 3 | protein | 377 | 37% helix, 22% strand | P19492 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, D, B, C
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, D, C
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.81 | 0.85 | 81 | SO4 |
| 2 | 1156 | 0.77 | 0.79 | 112 | SO4 |
| 3 | 623 | 0.67 | 0.77 | 56 | empty |
| 4 | 122 | 0.67 | 0.90 | 27 | empty |
| 5 | 146 | 0.63 | 0.86 | 27 | SO4 |
Interfaces
6 interfaces between chains.
- C–D · 1510 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1478 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 532 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 194 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 128 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 5FWY · Crystal structure of the AMPA receptor GluA2/A3 N-terminal domain heterodimer · the same entry in another collection · chain A against A, TM-score 1.00
- P19492 · AlphaFold monomer V2.0 prediction for glutamate receptor 3 (P19492) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P19491
- Every structure of UniProt P19492
- Elsewhere: RCSB PDB 5FWY · PDBe 5FWY · UniProt P19491 · UniProt P19492
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