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Cryo-EM structure of human full-length BETA3DELTA GABA(A)R in complex with nanobody NB25
Analyse Cryo-EM structure of human full-length BETA3DELTA GABA(A)R in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QN6
- Type
- protein
- Length
- 1,995 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-aminobutyric acid receptor subunit beta-3; Gamma-aminobutyric acid receptor subunit…
- UniProt
- P28472, O14764
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 32% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Gamma-aminobutyric acid receptor subunit beta-3 | protein | 327 | 38% helix, 31% strand | P28472 |
| E | Gamma-aminobutyric acid receptor subunit delta | protein | 324 | 37% helix, 30% strand | O14764 |
| K, L, M | Nanobody NB25 | protein | 121 | 2% helix, 54% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, B, K, C, L, D, M, E
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B, K, C, L, D, M
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, B, C, D
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 | 1155 | 0.83 | 0.84 | 116 | empty |
| 2 | 635 | 0.77 | 0.83 | 71 | empty |
| 3 | 609 | 0.75 | 0.82 | 57 | NAG |
| 4 | 643 | 0.74 | 0.81 | 60 | NAG |
| 5 | 365 | 0.74 | 0.85 | 53 | empty |
Interfaces
11 interfaces between chains.
- A–B · 2736 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2700 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 2671 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 2640 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 2443 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 glycan, 8 disulfide (N-glycosylation, disulfide).
Compared structures
- 7QN6 · Cryo-EM structure of human full-length beta3delta GABA(A)R in complex with nanobody Nb25 · the same entry in another collection · chain M against M, 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 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 P28472
- Every structure of UniProt O14764
- Elsewhere: RCSB PDB 7QN6 · PDBe 7QN6 · UniProt P28472 · UniProt O14764
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