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CryoEM structure of human rho1 GABAA receptor in complex with pregnenolone sulfate
Analyse CryoEM structure of human rho1 GABAA receptor in complex with pregnenolone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8RH9
- Type
- protein
- Length
- 1,665 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.21
- Source
- Homo sapiens
- Molecule
- Gamma-aminobutyric acid receptor subunit rho-1
- UniProt
- P24046
- Ligands
- D10, D12, A8W, NAG, CL
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · resolution 3.21 · 1 distinct chain · 37% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Gamma-aminobutyric acid receptor subunit rho-1 | protein | 333 | 37% helix, 31% strand | P24046 |
Ligands and binding sites
- D10 · Decane · ligand · 7 copies · chains A, E, C, D
- D12 · Dodecane · ligand · 3 copies · chains A, D
- A8W · Pregnenolone sulfate · ligand · chains A, B, C, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, C, D, E
- CL · Chloride ion · ion · chains B, C
- OCT · N-octane · additive · 16 copies · chains A, B, C, D, E
- HEX · Hexane · additive · 13 copies · chains A, B, C, D, E
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 | 1043 | 0.86 | 0.87 | 96 | A8W |
| 2 | 286 | 0.78 | 0.89 | 37 | empty |
| 3 | 654 | 0.78 | 0.83 | 92 | empty |
| 4 | 281 | 0.77 | 0.89 | 36 | empty |
| 5 | 274 | 0.76 | 0.88 | 38 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2730 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 2711 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2702 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 2701 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 2651 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- P24046 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor subunit rho-1… · a predicted model of the same protein · chain D against A, TM-score 0.88
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 P24046
- Elsewhere: RCSB PDB 8RH9 · PDBe 8RH9 · UniProt P24046
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