Research workbench
Human metabotropic GABA(B) receptor bound to agonist SKF97541 and positive allosteric modulator GS39783
Analyse Human metabotropic GABA(B) receptor bound to agonist SKF97541 and positive… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UO8
- Type
- protein
- Length
- 1,385 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-aminobutyric acid type B receptor subunit 1; Gamma-aminobutyric acid type B…
- UniProt
- Q9UBS5, O75899
- Ligands
- QD7, QDA, NAG, BMA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma-aminobutyric acid type B receptor subunit 1 | protein | 689 | 46% helix, 13% strand | Q9UBS5 |
| B | Gamma-aminobutyric acid type B receptor subunit 2 | protein | 696 | 43% helix, 13% strand | O75899 |
Ligands and binding sites
- QD7 · (R)-(3-aminopropyl)methylphosphinic acid · ligand · chains A
- QDA · N~4~,N~6~-dicyclopentyl-2-(methylsulfanyl)-5-nitropyrimidine-4,6-diamine · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.86 | 0.86 | 74 | empty |
| 2 | 1128 | 0.83 | 0.84 | 70 | empty |
| 3 | 985 | 0.78 | 0.80 | 83 | empty |
| 4 | 504 | 0.75 | 0.83 | 62 | QD7 |
| 5 | 322 | 0.74 | 0.86 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 1852 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 glycan, 7 disulfide (N-glycosylation, disulfide).
Compared structures
- 6UO8 · Human metabotropic GABA(B) receptor bound to agonist SKF97541 and positive allosteric… · the same entry in another collection · chain A against A, TM-score 1.00
- O75899 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid type B receptor subunit 2… · a predicted model of the same protein · chain B against A, TM-score 0.78
- Q9UBS5 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid type B receptor subunit 1… · a predicted model of the same protein · chain A against A, TM-score 0.74
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 Q9UBS5
- Every structure of UniProt O75899
- Elsewhere: RCSB PDB 6UO8 · PDBe 6UO8 · UniProt Q9UBS5 · UniProt O75899
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