Research workbench
Cryo-EM structure of human full-length ALPHA4BETA3GAMMA2 GABA(A)R in complex with GABA and nanobody NB25
Analyse Cryo-EM structure of human full-length ALPHA4BETA3GAMMA2 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
- 7QNA
- Type
- protein
- Length
- 1,763 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-aminobutyric acid receptor subunit alpha-4; Gamma-aminobutyric acid receptor…
- UniProt
- P48169, P28472, A0A1W2PQX1
- Ligands
- ABU, NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 34% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma-aminobutyric acid receptor subunit alpha-4 | protein | 333 | 39% helix, 30% strand | P48169 |
| B, D, E | Gamma-aminobutyric acid receptor subunit beta-3 | protein | 327 | 38% helix, 32% strand | P28472 |
| C | Gamma-aminobutyric acid receptor subunit gamma-2 | protein | 328 | 35% helix, 34% strand | A0A1W2PQX1 |
| N | Nanobody NB25 | protein | 121 | 7% helix, 48% strand | — |
Ligands and binding sites
- ABU · Gamma-amino-butanoic acid · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, D, E, N, C
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains B, D, E, N
- 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
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 | 747 | 0.82 | 0.86 | 65 | empty |
| 2 | 826 | 0.81 | 0.83 | 105 | empty |
| 3 | 657 | 0.75 | 0.81 | 77 | empty |
| 4 | 420 | 0.70 | 0.82 | 50 | NAG |
| 5 | 306 | 0.67 | 0.82 | 44 | empty |
Interfaces
7 interfaces between chains.
- A–E · 2981 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 2945 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 2845 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 2844 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2830 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 7QNA · Cryo-EM structure of human full-length alpha4beta3gamma2 GABA(A)R in complex with GABA… · the same entry in another collection · chain N against N, 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
- P48169 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor subunit alpha-4… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P48169
- Every structure of UniProt P28472
- Every structure of UniProt A0A1W2PQX1
- Elsewhere: RCSB PDB 7QNA · PDBe 7QNA · UniProt P48169 · UniProt P28472 · UniProt A0A1W2PQX1
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