Research workbench
Cryo-EM structure of human full-length synaptic ALPHA1BETA3GAMMA2 GABA(A)R in complex with RO15-4513 and megabody MB38
Analyse Cryo-EM structure of human full-length synaptic ALPHA1BETA3GAMMA2 GABA(A)R in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QNE
- Type
- protein
- Length
- 1,808 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GABA(A) receptor subunit alpha-1; Gamma-aminobutyric acid receptor subunit beta-3…
- UniProt
- A0A1B0GV38, P28472, A0A286YFI6
- Ligands
- D10, PIO, EIE, MAN, NAG, BMA, CL
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 6 distinct chains · 34% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GABA(A) receptor subunit alpha-1 | protein | 345 | 35% helix, 30% strand | A0A1B0GV38 |
| B | Gamma-aminobutyric acid receptor subunit beta-3 | protein | 334 | 37% helix, 31% strand | P28472 |
| C | GABA(A) receptor subunit gamma-2 | protein | 329 | 35% helix, 33% strand | A0A286YFI6 |
| D | GABA(A) receptor subunit alpha-1 | protein | 343 | 34% helix, 31% strand | A0A1B0GV38 |
| E | Gamma-aminobutyric acid receptor subunit beta-3 | protein | 334 | 38% helix, 31% strand | P28472 |
| G | Megabody MB38 | protein | 123 | 5% helix, 51% strand | — |
Ligands and binding sites
- D10 · Decane · ligand · 4 copies · chains A, B, C, D, E
- PIO · [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2, 3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate · ligand · 2 copies · chains A, D
- EIE · Ethyl 8-[(azanylidene-$L^{4}-azanylidene)amino]-5-methyl-6-oxidanylidene-4~{H}-imidazo[1,5-A][1, 4]benzodiazepine-3-carboxylate · ligand · chains C, D
- MAN · alpha-D-mannopyranose · sugar · 14 copies · chains C, D, B, A, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B, D, E, C
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains C, B, E
- CL · Chloride ion · ion · 3 copies · chains A, C, D
- OCT · N-octane · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.85 | 0.86 | 111 | CL |
| 2 | 794 | 0.79 | 0.82 | 78 | empty |
| 3 | 136 | 0.77 | 0.94 | 29 | empty |
| 4 | 458 | 0.71 | 0.81 | 64 | empty |
| 5 | 359 | 0.70 | 0.83 | 52 | EIE |
Interfaces
8 interfaces between chains.
- A–B · 2876 Ų buried · 25 hydrogen bonds · protein-protein
- A–E · 2858 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 2844 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2807 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 2678 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 7QNE · Cryo-EM structure of human full-length synaptic alpha1beta3gamma2 GABA(A)R in complex… · the same entry in another collection · chain G against G, TM-score 1.00
- P28472 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor subunit beta-3… · a predicted model of the same protein · chain E 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 A0A1B0GV38
- Every structure of UniProt P28472
- Every structure of UniProt A0A286YFI6
- Elsewhere: RCSB PDB 7QNE · PDBe 7QNE · UniProt A0A1B0GV38 · UniProt P28472 · UniProt A0A286YFI6
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