Research workbench
Crystal structure of the extracellular domain of human GABA(B) receptor bound to the antagonist SCH50911
Analyse Crystal structure of the extracellular domain of human GABA(B) receptor bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MR9
- Type
- protein
- Length
- 810 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.35
- Source
- Homo sapiens
- Molecule
- Gamma-aminobutyric acid type B receptor subunit 1; Gamma-aminobutyric acid type B…
- UniProt
- Q9UBS5, O75899
- Ligands
- 2BX, NAG, FUC, MAN
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · resolution 2.35 · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma-aminobutyric acid type B receptor subunit 1 | protein | 407 | 38% helix, 22% strand | Q9UBS5 |
| B | Gamma-aminobutyric acid type B receptor subunit 2 | protein | 403 | 39% helix, 23% strand | O75899 |
Ligands and binding sites
- 2BX · [(2S)-5,5-dimethylmorpholin-2-yl]acetic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.69 | 0.77 | 82 | 2BX |
| 2 | 251 | 0.59 | 0.79 | 45 | empty |
| 3 | 164 | 0.50 | 0.78 | 19 | empty |
| 4 | 87 | 0.43 | 0.80 | 21 | empty |
| 5 | 56 | 0.42 | 0.82 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 750 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4MR9 · Crystal structure of the extracellular domain of human GABA(B) receptor bound to the… · 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 0.99
- 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 0.99
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 4MR9 · PDBe 4MR9 · UniProt Q9UBS5 · UniProt O75899
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