Research workbench
Structure of a chimaeric BETA3-ALPHA5 gabaa receptor in complex with nanobody NB25
Analyse Structure of a chimaeric BETA3-ALPHA5 gabaa receptor in complex with nanobody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OJM
- Type
- protein
- Length
- 2,270 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human gabaa receptor chimera BETA3-ALPHA5,GAMMA- aminobutyric acid receptor subunit…
- UniProt
- P28472, P31644
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Human gabaa receptor chimera BETA3-ALPHA5,GAMMA- aminobutyric acid receptor subunit beta-3,GAMMA-aminobutyric acid receptor subunit alpha-5 | protein | 330 | 39% helix, 32% strand | P28472, P31644 |
| B | Human gabaa receptor chimera BETA3-ALPHA5,GAMMA- aminobutyric acid receptor subunit beta-3,GAMMA-aminobutyric acid receptor subunit alpha-5 | protein | 333 | 39% helix, 32% strand | P28472, P31644 |
| D | Human gabaa receptor chimera BETA3-ALPHA5,GAMMA- aminobutyric acid receptor subunit beta-3,GAMMA-aminobutyric acid receptor subunit alpha-5 | protein | 332 | 39% helix, 32% strand | P28472, P31644 |
| K, L, M, N, O | Nanobody NB25 | protein | 123 | 5% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, K, B, L, C, M, D, N, E, O
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains A, L, C, 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 | 900 | 0.78 | 0.81 | 92 | empty |
| 2 | 536 | 0.73 | 0.82 | 72 | empty |
| 3 | 245 | 0.73 | 0.87 | 43 | empty |
| 4 | 289 | 0.72 | 0.85 | 48 | empty |
| 5 | 365 | 0.71 | 0.83 | 56 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2719 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2647 Ų buried · 23 hydrogen bonds · protein-protein
- A–E · 2562 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 2545 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 2527 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 5OJM · Structure of a chimaeric beta3-alpha5 GABAA receptor in complex with nanobody Nb25 · the same entry in another collection · chain O against O, 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 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 P28472
- Every structure of UniProt P31644
- Elsewhere: RCSB PDB 5OJM · PDBe 5OJM · UniProt P28472 · UniProt P31644
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