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Crystal structure of a human gamma-aminobutyric acid receptor, the GABA(A)R-BETA3 homopentamer
Analyse Crystal structure of a human gamma-aminobutyric acid receptor, the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4COF
- Type
- protein
- Length
- 1,665 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-aminobutyric acid receptor subunit beta-3
- UniProt
- P28472
- Ligands
- BEN, NAG, BMA, CL
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma-aminobutyric acid receptor subunit beta-3 | protein | 340 | 38% helix, 31% strand | P28472 |
| B, C, E | Gamma-aminobutyric acid receptor subunit beta-3 | protein | 331 | 37% helix, 32% strand | P28472 |
| D | Gamma-aminobutyric acid receptor subunit beta-3 | protein | 332 | 38% helix, 32% strand | P28472 |
Ligands and binding sites
- BEN · Benzamidine · ligand · 5 copies · chains A, E, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D, E
- BMA · beta-D-mannopyranose · sugar · 5 copies
- CL · Chloride ion · ion · 5 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.77 | 0.83 | 52 | empty |
| 2 | 511 | 0.75 | 0.83 | 59 | BEN |
| 3 | 737 | 0.75 | 0.80 | 72 | BEN |
| 4 | 647 | 0.74 | 0.81 | 67 | BEN |
| 5 | 574 | 0.74 | 0.81 | 56 | BEN |
Interfaces
5 interfaces between chains.
- A–B · 2686 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 2618 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 2614 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 2556 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 2556 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 4COF · Crystal structure of a human gamma-aminobutyric acid receptor, the GABA(A)R-beta3… · the same entry in another collection · chain E against E, TM-score 1.00
- P28472 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor subunit beta-3… · a predicted model of the same protein · chain D 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 P28472
- Elsewhere: RCSB PDB 4COF · PDBe 4COF · UniProt P28472
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