MolNFT v1 · #129037 · protein
Structure of a chimaeric BETA3-ALPHA5 gabaa receptor in complex with nanobody NB25 and pregnanolone
5O8F · Gamma-aminobutyric acid receptor subunit beta-3,GAMMA…: “Structure of a chimaeric BETA3-ALPHA5 gabaa receptor in complex with nanobody NB25 and pregnanolone”. X-ray diffraction, 4 ligands (P9N, MAN, NAG), 20 pockets (best…
- PDB
- 5O8F
- Type
- protein
- Length
- 2,282 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-aminobutyric acid receptor subunit beta-3,GAMMA- aminobutyric acid receptor subunit…
- UniProt
- P28472, P31644
- Ligands
- P9N, MAN, NAG, BMA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Gamma-aminobutyric acid receptor subunit beta-3,GAMMA- aminobutyric acid receptor subunit alpha-5,GAMMA-aminobutyric acid receptor subunit alpha-5 | protein | 332 | 39% helix, 32% strand | P28472, P31644 |
| K, O | Nanobody NB25 | protein | 125 | 5% helix, 52% strand | — |
| L, M, N | Nanobody NB25 | protein | 124 | 5% helix, 51% strand | — |
Ligands and binding sites
- P9N · Pregnanolone · ligand · 5 copies · chains B, C, D, E, A
- MAN · alpha-D-mannopyranose · sugar · 20 copies · chains A, K, B, L, C, M, D, N, E, O
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, K, B, L, C, M, D, N, E, O
- BMA · beta-D-mannopyranose · sugar · 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.79 | 0.81 | 74 | empty |
| 2 | 73 | 0.72 | 0.97 | 25 | empty |
| 3 | 381 | 0.72 | 0.83 | 57 | empty |
| 4 | 383 | 0.71 | 0.83 | 53 | empty |
| 5 | 381 | 0.70 | 0.82 | 55 | empty |
Interfaces
15 interfaces between chains.
- A–E · 2652 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2644 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 2641 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 2639 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 2626 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- P28472 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor subunit beta-3… · a predicted model of the same protein · chain E against A, TM-score 0.98
- P31644 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor subunit alpha-5… · a predicted model of the same protein · chain C 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
- Every structure of UniProt P31644
- Elsewhere: RCSB PDB 5O8F · PDBe 5O8F · UniProt P28472 · UniProt P31644
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