MolNFT v1 · #146892 · protein
Cryo-EM structure of the benzodiazepine-sensitive ALPHA1BETA1GAMMA2S tri-heteromeric gabaa receptor in complex with GABA (ecd MAP)
6DW1 · 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), 12 pockets (best…
- PDB
- 6DW1
- Type
- protein
- Length
- 1,046 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
- 12 · best druggability 0.72
Structure
electron microscopy · 4 distinct chains · 7% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Gamma-aminobutyric acid receptor subunit gamma-2 | protein | 208 | 5% helix, 39% strand | P18508 |
| C, A | Gamma-aminobutyric acid receptor subunit alpha-1,GAMMA- aminobutyric acid receptor subunit alpha-1 | protein | 210 | 6% helix, 44% strand | P62813 |
| E | Gamma-aminobutyric acid receptor subunit beta-1,GAMMA- aminobutyric acid receptor subunit beta-1 | protein | 208 | 9% helix, 42% strand | P15431 |
| B | Gamma-aminobutyric acid receptor subunit beta-1,GAMMA- aminobutyric acid receptor subunit beta-1 | protein | 210 | 9% helix, 42% strand | P15431 |
Ligands and binding sites
- ABU · Gamma-amino-butanoic acid · ligand · 3 copies · chains C, B, A, E
- 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, B, D, E
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 654 | 0.72 | 0.79 | 64 | empty |
| 2 | 493 | 0.69 | 0.80 | 53 | ABU |
| 3 | 80 | 0.64 | 0.91 | 20 | empty |
| 4 | 384 | 0.61 | 0.77 | 51 | empty |
| 5 | 281 | 0.61 | 0.80 | 43 | empty |
Interfaces
5 interfaces between chains.
- A–E · 1550 Ų buried · 17 hydrogen bonds · protein-protein
- C–B · 1550 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1494 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 1310 Ų buried · 18 hydrogen bonds · protein-protein
- D–C · 1261 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 6DW1 · 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 E against A, TM-score 0.99
- 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 0.99
- 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 0.97
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 P18508
- Every structure of UniProt P62813
- Every structure of UniProt P15431
- Elsewhere: RCSB PDB 6DW1 · PDBe 6DW1 · UniProt P18508 · UniProt P62813 · UniProt P15431
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