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Structure of the AMPAR GluA3 N-terminal domain bound to phosphate
Analyse Structure of the AMPAR GluA3 N-terminal domain bound to phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FPJ
- Type
- protein
- Length
- 1,118 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.96
- Source
- Rattus norvegicus
- Molecule
- Glutamate receptor 3
- UniProt
- P19492
- Ligands
- NAG, PO4
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · resolution 1.96 · 3 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor 3 | protein | 374 | 37% helix, 23% strand | P19492 |
| B | Glutamate receptor 3 | protein | 379 | 37% helix, 23% strand | P19492 |
| C | Glutamate receptor 3 | protein | 365 | 37% helix, 23% strand | P19492 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 7 copies · chains A, B, C
- DMS · Dimethyl sulfoxide · additive · 7 copies · chains A, C, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.76 | 0.79 | 116 | DMS |
| 2 | 1037 | 0.73 | 0.76 | 96 | PO4, NAG, DMS |
| 3 | 334 | 0.66 | 0.81 | 31 | DMS |
| 4 | 303 | 0.66 | 0.81 | 27 | DMS |
| 5 | 334 | 0.65 | 0.80 | 25 | DMS |
Interfaces
3 interfaces between chains.
- A–C · 1672 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 443 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 282 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
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 P19492
- Elsewhere: RCSB PDB 6FPJ · PDBe 6FPJ · UniProt P19492
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