MolNFT v1 · #146891 · protein
Cryo-EM structure of the benzodiazepine-sensitive ALPHA1BETA1GAMMA2S tri-heteromeric gabaa receptor in complex with GABA (whole MAP)
6DW0 · Gamma-aminobutyric acid receptor subunit gamma-2: “Cryo-EM structure of the benzodiazepine-sensitive ALPHA1BETA1GAMMA2S tri-heteromeric gabaa receptor in…”. Electron microscopy, 4 ligands (ABU, NAG, MAN), 20 pockets (best…
- PDB
- 6DW0
- Type
- protein
- Length
- 1,529 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-aminobutyric acid receptor subunit gamma-2; Gamma-aminobutyric acid receptor…
- UniProt
- P18508, P62813, P15431
- Ligands
- ABU, NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Gamma-aminobutyric acid receptor subunit gamma-2 | protein | 299 | 25% helix, 28% strand | P18508 |
| C, A | Gamma-aminobutyric acid receptor subunit alpha-1,GAMMA- aminobutyric acid receptor subunit alpha-1 | protein | 296 | 29% helix, 33% strand | P62813 |
| E, B | Gamma-aminobutyric acid receptor subunit beta-1,GAMMA- aminobutyric acid receptor subunit beta-1 | protein | 319 | 37% helix, 31% strand | P15431 |
Ligands and binding sites
- ABU · Gamma-amino-butanoic acid · ligand · 3 copies · chains A, E, C, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains C, B, A, E
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains A, D, E
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains D, E, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.87 | 0.89 | 129 | empty |
| 2 | 684 | 0.87 | 0.91 | 104 | empty |
| 3 | 464 | 0.84 | 0.91 | 93 | empty |
| 4 | 320 | 0.75 | 0.87 | 47 | ABU |
| 5 | 197 | 0.74 | 0.90 | 39 | empty |
Interfaces
6 interfaces between chains.
- A–E · 2311 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2230 Ų buried · 10 hydrogen bonds · protein-protein
- C–B · 2191 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 2045 Ų buried · 15 hydrogen bonds · protein-protein
- D–C · 1934 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 6DW0 · Cryo-EM structure of the benzodiazepine-sensitive alpha1beta1gamma2S tri-heteromeric… · the same entry in another collection · chain B against B, TM-score 1.00
- P15431 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor subunit beta-1… · a predicted model of the same protein · chain B against A, TM-score 0.98
- P62813 · 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 0.97
- P18508 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor subunit gamma-2… · a predicted model of the same protein · chain D against A, TM-score 0.96
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 P18508
- Every structure of UniProt P62813
- Every structure of UniProt P15431
- Elsewhere: RCSB PDB 6DW0 · PDBe 6DW0 · UniProt P18508 · UniProt P62813 · UniProt P15431
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