Research workbench
Cryo-EM structure of the human synaptic alpha1-beta3-gamma2 GABAA receptor in complex with Megabody38 in a lipid nanodisc
Analyse Cryo-EM structure of the human synaptic alpha1-beta3-gamma2 GABAA receptor in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I53
- Type
- protein
- Length
- 1,821 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Homo sapiens; Lama glama
- Molecule
- Gamma-aminobutyric acid receptor subunit beta-3; Gamma-aminobutyric acid receptor subunit…
- UniProt
- P28472, P14867, P18507
- Ligands
- POV, PIO, NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · resolution 3.2 · 6 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Gamma-aminobutyric acid receptor subunit beta-3 | protein | 336 | 36% helix, 28% strand | P28472 |
| A | Gamma-aminobutyric acid receptor subunit alpha-1 | protein | 349 | 31% helix, 27% strand | P14867 |
| B | Gamma-aminobutyric acid receptor subunit beta-3 | protein | 338 | 35% helix, 31% strand | P28472 |
| C | Gamma-aminobutyric acid receptor subunit gamma-2 | protein | 328 | 32% helix, 33% strand | P18507 |
| D | Gamma-aminobutyric acid receptor subunit alpha-1 | protein | 347 | 32% helix, 27% strand | P14867 |
| G | Megabody38 | protein | 123 | 5% helix, 50% strand | — |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 3 copies · chains E, A, B, D
- 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
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains E, A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 11 copies · chains E, C, B, A
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains E, C, 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.86 | 0.86 | 113 | empty |
| 2 | 793 | 0.85 | 0.88 | 82 | empty |
| 3 | 525 | 0.68 | 0.78 | 70 | empty |
| 4 | 110 | 0.67 | 0.90 | 21 | empty |
| 5 | 358 | 0.66 | 0.80 | 49 | empty |
Interfaces
7 interfaces between chains.
- A–B · 3197 Ų buried · 14 hydrogen bonds · protein-protein
- E–D · 3152 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 3025 Ų buried · 21 hydrogen bonds · protein-protein
- E–A · 2779 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 2691 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 6I53 · Cryo-EM structure of the human synaptic ALPHA1-BETA3-GAMMA2 gabaa receptor in complex… · the same entry in another collection · chain G against G, 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
- P14867 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor subunit alpha-1… · a predicted model of the same protein · chain D 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 P28472
- Every structure of UniProt P14867
- Every structure of UniProt P18507
- Elsewhere: RCSB PDB 6I53 · PDBe 6I53 · UniProt P28472 · UniProt P14867 · UniProt P18507
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