Research workbench
Structure of the complex of lbd-tmd part of AMPA receptor GLUA2 with auxiliary subunit tarp gamma-5 bound to agonist quisqualate
Analyse Structure of the complex of lbd-tmd part of AMPA receptor GLUA2 with auxiliary… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RZ8
- Type
- protein
- Length
- 2,044 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- PCW, QUS
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor 2 | protein | 609 | 53% helix, 11% strand | P19491 |
| B, D | Glutamate receptor 2 | protein | 413 | 47% helix, 9% strand | P19491 |
Ligands and binding sites
- PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 22 copies · chains A, D, B, C
- QUS · (S)-2-amino-3-(3,5-dioxo-[1,2,4]oxadiazolidin-2-yl)-propionic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1124 | 0.86 | 0.87 | 123 | empty |
| 2 | 194 | 0.81 | 0.95 | 21 | empty |
| 3 | 1183 | 0.78 | 0.79 | 101 | empty |
| 4 | 770 | 0.78 | 0.82 | 73 | empty |
| 5 | 246 | 0.75 | 0.89 | 42 | empty |
Interfaces
6 interfaces between chains.
- A–D · 3081 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 2976 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 2910 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 2908 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 32 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7RZ8 · Structure of the complex of LBD-TMD part of AMPA receptor GluA2 with auxiliary subunit… · the same entry in another collection · chain D against D, TM-score 1.00
- P19491 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P19491) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 7RZ8 · PDBe 7RZ8 · UniProt P19491
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.