Research workbench
LBD conformation 2 (LBDconf2) of GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma2, with 10mM CaCl2, 140mM NMDG, 330uM CTZ, and 100mM L-glutamate (Open-Ca10)
Analyse LBD conformation 2 (LBDconf2) of GluA2 flip Q isoform of AMPA receptor in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8FQE
- Type
- protein
- Length
- 1,060 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.14
- Source
- Rattus norvegicus
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- GLU, CYZ
- Pockets
- 13 · best druggability 0.79
Structure
electron microscopy · resolution 3.14 · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor 2 | protein | 260 | 37% helix, 22% strand | P19491 |
| B, D | Glutamate receptor 2 | protein | 270 | 35% helix, 23% strand | P19491 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 4 copies · chains A, B, C, D
- CYZ · Cyclothiazide · ligand · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 839 | 0.79 | 0.82 | 91 | CYZ |
| 2 | 737 | 0.77 | 0.81 | 83 | CYZ |
| 3 | 50 | 0.69 | 0.98 | 17 | GLU |
| 4 | 280 | 0.57 | 0.78 | 30 | empty |
| 5 | 413 | 0.56 | 0.74 | 36 | empty |
Interfaces
4 interfaces between chains.
- A–D · 900 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 861 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 139 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 108 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- P19491 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P19491) · a predicted model of the same protein · chain A 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
- Elsewhere: RCSB PDB 8FQE · PDBe 8FQE · UniProt P19491
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