Research workbench
Human metabotropic GABA(B) receptor in its apo state
Analyse Human metabotropic GABA(B) receptor in its apo state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VJM
- Type
- protein
- Length
- 1,369 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
- NAG, FUC
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma-aminobutyric acid type B receptor subunit 1 | protein | 684 | 46% helix, 14% strand | Q9UBS5 |
| B | Gamma-aminobutyric acid type B receptor subunit 2 | protein | 685 | 49% helix, 13% strand | O75899 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1172 | 0.86 | 0.87 | 108 | empty |
| 2 | 1094 | 0.84 | 0.85 | 111 | empty |
| 3 | 189 | 0.75 | 0.90 | 33 | empty |
| 4 | 332 | 0.69 | 0.82 | 41 | empty |
| 5 | 131 | 0.68 | 0.89 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1008 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6VJM · Human metabotropic GABA(B) receptor in its apo state · 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 0.92
- 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 0.82
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 6VJM · PDBe 6VJM · UniProt Q9UBS5 · UniProt O75899
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