Research workbench
Desensitized state of GLUA1/2 AMPA receptor in complex with tarp-gamma 8 (tmd-lbd)
Analyse Desensitized state of GLUA1/2 AMPA receptor in complex with tarp-gamma 8… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QHH
- Type
- protein
- Length
- 1,978 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform flip of glutamate receptor 1; Isoform flip of glutamate receptor 2…
- UniProt
- P19490, P19491, Q8VHW5
- Ligands
- PAM, GLU, 79N
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Isoform flip of glutamate receptor 1 | protein | 400 | 49% helix, 13% strand | P19490 |
| B, D | Isoform flip of glutamate receptor 2 | protein | 404 | 49% helix, 13% strand | P19491 |
| J, I | Voltage-dependent calcium channel gamma-8 subunit | protein | 185 | 63% helix, 11% strand | Q8VHW5 |
Ligands and binding sites
- PAM · Palmitoleic acid · ligand · 10 copies · chains A, B, C, D, J, I
- GLU · Glutamic acid · ligand · 4 copies · chains A, B, C, D
- 79N · (2S)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate · ligand · 2 copies · chains B, C, A, D
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 2 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 910 | 0.86 | 0.88 | 149 | GLU |
| 2 | 747 | 0.84 | 0.87 | 118 | GLU |
| 3 | 301 | 0.77 | 0.89 | 58 | GLU |
| 4 | 204 | 0.76 | 0.91 | 37 | empty |
| 5 | 205 | 0.76 | 0.90 | 29 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2415 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 2415 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 2199 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 2196 Ų buried · 10 hydrogen bonds · protein-protein
- A–J · 809 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7QHH · Desensitized state of GluA1/2 AMPA receptor in complex with TARP-gamma 8 (TMD-LBD) · the same entry in another collection · chain I against I, TM-score 1.00
- Q8VHW5 · AlphaFold monomer V2.0 prediction for voltage-dependent calcium channel gamma-8 subunit… · a predicted model of the same protein · chain J against A, TM-score 0.94
- P19491 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P19491) · a predicted model of the same protein · chain D against A, TM-score 0.86
- P19490 · AlphaFold monomer V2.0 prediction for glutamate receptor 1 (P19490) · a predicted model of the same protein · chain C against A, TM-score 0.63
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 P19490
- Every structure of UniProt P19491
- Every structure of UniProt Q8VHW5
- Elsewhere: RCSB PDB 7QHH · PDBe 7QHH · UniProt P19490 · UniProt P19491 · UniProt Q8VHW5
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