MolNFT v1 · #100236 · protein
Crystal structure of the extracellular domain of human GABA(B) receptor bound to the antagonist phaclofen
4MRM · Gamma-aminobutyric acid type B receptor subunit 1: “Crystal structure of the extracellular domain of human GABA(B) receptor bound to the antagonist phaclofen”. X-ray diffraction, 4 ligands (2BY, NAG, MAN), 8 pockets (best…
- PDB
- 4MRM
- Type
- protein
- Length
- 807 residues
- Chains
- 2
- Method
- x-ray diffraction
- 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
- 2BY, NAG, MAN, BMA
- Pockets
- 8 · best druggability 0.62
Structure
x-ray diffraction · 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, 21% strand | Q9UBS5 |
| B | Gamma-aminobutyric acid type B receptor subunit 2 | protein | 400 | 39% helix, 23% strand | O75899 |
Ligands and binding sites
- 2BY · phaclofen · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.62 | 0.77 | 61 | 2BY |
| 2 | 292 | 0.59 | 0.78 | 48 | empty |
| 3 | 66 | 0.49 | 0.85 | 20 | empty |
| 4 | 158 | 0.48 | 0.77 | 20 | empty |
| 5 | 145 | 0.44 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 743 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4MRM · Crystal structure of the extracellular domain of human GABA(B) receptor bound to the… · the same entry in another collection · chain B against B, 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 0.97
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 4MRM · PDBe 4MRM · UniProt Q9UBS5 · UniProt O75899
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