MolNFT v1 · #169195 · protein
Human gabaa receptor ALPHA1-BETA2-GAMMA2 subtype in complex with GABA plus etomidate
6X3V · Gamma-aminobutyric acid receptor subunit beta-2: “Human gabaa receptor ALPHA1-BETA2-GAMMA2 subtype in complex with GABA plus etomidate”. Electron microscopy, 5 ligands (ABU, V8D, NAG), 20 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 6X3V
- Type
- protein
- Length
- 2,121 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-aminobutyric acid receptor subunit beta-2; Gamma-aminobutyric acid receptor subunit…
- UniProt
- P47870, P14867, P18507
- Ligands
- ABU, V8D, NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 7 distinct chains · 25% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Gamma-aminobutyric acid receptor subunit beta-2 | protein | 334 | 35% helix, 27% strand | P47870 |
| B, D | Gamma-aminobutyric acid receptor subunit alpha-1 | protein | 338 | 37% helix, 28% strand | P14867 |
| E | Gamma-aminobutyric acid receptor subunit gamma-2 | protein | 333 | 35% helix, 30% strand | P18507 |
| I | Kappa Fab light chain | protein | 105 | 0% helix, 45% strand | — |
| J | IGG2B Fab heavy chain | protein | 116 | 3% helix, 48% strand | — |
| L | Kappa Fab light chain | protein | 106 | 0% helix, 42% strand | — |
| K | IGG2B Fab heavy chain | protein | 117 | 3% helix, 53% strand | — |
Ligands and binding sites
- ABU · Gamma-amino-butanoic acid · ligand · 2 copies · chains A, B, C, D
- V8D · Ethyl 1-[(1R)-1-phenylethyl]-1H-imidazole-5-carboxylate · ligand · 2 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D, E
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains A, E, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1094 | 0.87 | 0.88 | 113 | V8D |
| 2 | 717 | 0.73 | 0.79 | 58 | empty |
| 3 | 580 | 0.73 | 0.81 | 73 | empty |
| 4 | 484 | 0.73 | 0.82 | 65 | empty |
| 5 | 594 | 0.70 | 0.79 | 50 | empty |
Interfaces
11 interfaces between chains.
- A–E · 2921 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 2902 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2779 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 2760 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 2430 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 6X3V · Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus etomidate · the same entry in another collection · chain K against K, TM-score 1.00
- P47870 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor subunit beta-2… · a predicted model of the same protein · chain C 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 E 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 P47870
- Every structure of UniProt P14867
- Every structure of UniProt P18507
- Elsewhere: RCSB PDB 6X3V · PDBe 6X3V · UniProt P47870 · UniProt P14867 · UniProt P18507
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