MolNFT v2 · #217779 · protein
Crystal structure of the AMPA receptor GluA2-L504Y-N775S ligand binding domain in complex with L-glutamate and positive allosteric modulator BPAM395 at 1.55A resolution
8QEZ · Glutamate receptor 2: “Crystal structure of the AMPA receptor GluA2-L504Y-N775S ligand binding domain in complex with L-glutamate…”. X-ray diffraction at 1.55, 4 ligands (GLU, UF5, ZN), 6 pockets (best druggability 0.83). MolNFT v2…
- PDB
- 8QEZ
- Type
- protein
- Length
- 792 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.55
- Source
- Rattus norvegicus
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- GLU, UF5, ZN, CL
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · resolution 1.55 · 1 distinct chain · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glutamate receptor 2 | protein | 264 | 37% helix, 20% strand | P19491 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 3 copies · chains A, B, C
- UF5 · 6-chloranyl-4-cyclopropyl-2,3-dihydrothieno[3,2-e][1,2,4]thiadiazine 1,1-dioxide · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 7 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- ACT · Acetate ion · additive · 8 copies · chains A, B, C
- GOL · Glycerol · additive · 4 copies · chains A, B, C
- CAC · Cacodylate ion · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1001 | 0.83 | 0.84 | 119 | UF5, CL, ACT, GOL |
| 2 | 266 | 0.58 | 0.79 | 32 | empty |
| 3 | 172 | 0.44 | 0.75 | 26 | CL |
| 4 | 97 | 0.39 | 0.76 | 23 | empty |
| 5 | 85 | 0.39 | 0.77 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 994 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 355 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 77 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- P19491 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P19491) · 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
- Elsewhere: RCSB PDB 8QEZ · PDBe 8QEZ · UniProt P19491
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