MolNFT v1 · #151664 · protein
Cryoem structure of human full-length heteromeric ALPHA1BETA3GAMMA2L GABA(A)R in complex with picrotoxin, GABA and megabody MB38.
6HUJ · Gamma-aminobutyric acid receptor subunit alpha-1,GAMMA…: “Cryoem structure of human full-length heteromeric ALPHA1BETA3GAMMA2L GABA(A)R in complex with picrotoxin…”. Electron microscopy, 6 ligands (PIO, ABU, RI5), 20 pockets (best…
- PDB
- 6HUJ
- Type
- protein
- Length
- 1,812 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-aminobutyric acid receptor subunit alpha-1,GAMMA- aminobutyric acid receptor…
- UniProt
- P08219, P14867, P28472, P18507
- Ligands
- PIO, ABU, RI5, NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 6 distinct chains · 32% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma-aminobutyric acid receptor subunit alpha-1,GAMMA- aminobutyric acid receptor subunit alpha-1 | protein | 347 | 34% helix, 27% strand | P08219, P14867 |
| B | Gamma-aminobutyric acid receptor subunit beta-3 | protein | 336 | 34% helix, 29% strand | P28472 |
| C | Gamma-aminobutyric acid receptor subunit gamma-2 | protein | 330 | 32% helix, 31% strand | P18507 |
| D | Gamma-aminobutyric acid receptor subunit alpha-1,GAMMA- aminobutyric acid receptor subunit alpha-1 | protein | 344 | 32% helix, 29% strand | P08219, P14867 |
| E | Gamma-aminobutyric acid receptor subunit beta-3 | protein | 334 | 37% helix, 28% strand | P28472 |
| G | Megabody MB38 | protein | 121 | 5% helix, 48% strand | — |
Ligands and binding sites
- PIO · [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2, 3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate · ligand · 2 copies · chains A, D
- ABU · Gamma-amino-butanoic acid · ligand · 2 copies · chains A, B, D, E
- RI5 · (1aR,2aR,3S,6R,6aS,8aS,8bR,9R)-2a-hydroxy-8b-methyl-9-(prop-1-en-2-yl)hexahydro-3,6-methano-1,5,7-trioxacyclopenta[ij]c yclopropa[a]azulene-4,8(3H)-dione · ligand · chains A, B, C, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B, C, D, E
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains C, D, B, A, E
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains C, B, 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 899 | 0.81 | 0.83 | 103 | empty |
| 2 | 1031 | 0.80 | 0.82 | 100 | empty |
| 3 | 146 | 0.79 | 0.96 | 29 | RI5 |
| 4 | 74 | 0.73 | 0.97 | 18 | empty |
| 5 | 72 | 0.73 | 0.97 | 24 | empty |
Interfaces
8 interfaces between chains.
- A–B · 3242 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 3185 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 3052 Ų buried · 23 hydrogen bonds · protein-protein
- A–E · 2963 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2881 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 6HUJ · CryoEM structure of human full-length heteromeric alpha1beta3gamma2L GABA(A)R in complex… · the same entry in another collection · chain D against D, TM-score 1.00
- P14867 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor subunit alpha-1… · a predicted model of the same protein · chain A against A, TM-score 0.99
- P08219 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor subunit alpha-1… · a predicted model of the same protein · chain A against A, TM-score 0.99
- P18507 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor subunit gamma-2… · a predicted model of the same protein · chain C against A, TM-score 0.99
- 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 0.99
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 P08219
- Every structure of UniProt P14867
- Every structure of UniProt P28472
- Every structure of UniProt P18507
- Elsewhere: RCSB PDB 6HUJ · PDBe 6HUJ · UniProt P08219 · UniProt P14867 · UniProt P28472 · UniProt P18507
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