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Structure of the complex of lbd-tmd part of AMPA receptor GLUA2 with auxiliary subunit tarp gamma-5 bound to agonist glutamate
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
- 7RYY
- Type
- protein
- Length
- 2,020 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- GLU, PCW
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 2 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor 2 | protein | 602 | 52% helix, 14% strand | P19491 |
| B, D | Glutamate receptor 2 | protein | 408 | 47% helix, 11% strand | P19491 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 4 copies · chains A, B, C, D
- PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.80 | 0.83 | 77 | empty |
| 2 | 341 | 0.80 | 0.90 | 55 | empty |
| 3 | 686 | 0.79 | 0.84 | 70 | empty |
| 4 | 449 | 0.78 | 0.86 | 60 | empty |
| 5 | 1041 | 0.77 | 0.79 | 78 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2780 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 2682 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 2676 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2613 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 22 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7RYY · Structure of the complex of LBD-TMD part of AMPA receptor GluA2 with auxiliary subunit… · the same entry in another collection · chain B against B, 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 7RYY · PDBe 7RYY · UniProt P19491
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