Research workbench
CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with diazepam (Valium), GABA and megabody Mb38.
Analyse CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HUP
- Type
- protein
- Length
- 1,808 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.58
- Source
- Bos taurus; Homo sapiens; Lama glama
- Molecule
- Gamma-aminobutyric acid receptor subunit alpha-1,Gamma-aminobutyric acid receptor subunit…
- UniProt
- P08219, P14867, P28472, P18507
- Ligands
- DZP, PIO, ABU, NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · resolution 3.58 · 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 | 344 | 34% helix, 28% strand | P08219, P14867 |
| B | Gamma-aminobutyric acid receptor subunit beta-3 | protein | 336 | 34% helix, 27% strand | P28472 |
| C | Gamma-aminobutyric acid receptor subunit gamma-2 | protein | 330 | 34% helix, 33% strand | P18507 |
| D | Gamma-aminobutyric acid receptor subunit alpha-1,Gamma-aminobutyric acid receptor subunit alpha-1 | protein | 343 | 31% helix, 28% strand | P08219, P14867 |
| E | Gamma-aminobutyric acid receptor subunit beta-3 | protein | 334 | 38% helix, 27% strand | P28472 |
| G | Megabody Mb38 | protein | 121 | 2% helix, 46% strand | — |
Ligands and binding sites
- DZP · 7-chloro-1-methyl-5-phenyl-1,3-dihydro-2H-1,4-benzodiazepin-2-one · ligand · 3 copies · chains A, B, C, D, E
- 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
- 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.85 | 0.86 | 86 | DZP |
| 2 | 964 | 0.82 | 0.83 | 120 | empty |
| 3 | 570 | 0.75 | 0.82 | 75 | empty |
| 4 | 197 | 0.74 | 0.89 | 27 | DZP |
| 5 | 346 | 0.68 | 0.82 | 43 | DZP |
Interfaces
7 interfaces between chains.
- A–B · 3049 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 2967 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 2927 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 2844 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 2618 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 6HUP · Cryoem structure of human full-length ALPHA1BETA3GAMMA2L GABA(A)R in complex with… · 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 B 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
- 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
- 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 0.98
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 6HUP · PDBe 6HUP · UniProt P08219 · UniProt P14867 · UniProt P28472 · UniProt P18507
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