Research workbench
Cryo-EM structure of human full-length BETA3GAMMA2 GABA(A)R in complex with GABA and nanobody NB25
Analyse Cryo-EM structure of human full-length BETA3GAMMA2 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
- 7QNB
- Type
- protein
- Length
- 1,767 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-aminobutyric acid type a receptor subunit GAMMA2; Gamma-aminobutyric acid receptor…
- UniProt
- A0A2K5TLN2, P28472
- Ligands
- ABU, NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 3 distinct chains · 32% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Gamma-aminobutyric acid type a receptor subunit GAMMA2 | protein | 328 | 35% helix, 33% strand | A0A2K5TLN2 |
| B, D, E | Gamma-aminobutyric acid receptor subunit beta-3 | protein | 330 | 38% helix, 31% strand | P28472 |
| N | Nanobody NB25 | protein | 121 | 7% helix, 49% strand | — |
Ligands and binding sites
- ABU · Gamma-amino-butanoic acid · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains B, D, E, N, A, C
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains B, D, E, N
- BMA · beta-D-mannopyranose · sugar · 3 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 650 | 0.81 | 0.86 | 61 | empty |
| 2 | 397 | 0.75 | 0.85 | 60 | empty |
| 3 | 418 | 0.71 | 0.82 | 45 | NAG |
| 4 | 536 | 0.70 | 0.80 | 63 | empty |
| 5 | 418 | 0.70 | 0.81 | 46 | empty |
Interfaces
7 interfaces between chains.
- A–E · 2939 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 2937 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 2877 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 2863 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 2804 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 7QNB · Cryo-EM structure of human full-length beta3gamma2 GABA(A)R in complex with GABA and… · 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 E 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 A0A2K5TLN2
- Every structure of UniProt P28472
- Elsewhere: RCSB PDB 7QNB · PDBe 7QNB · UniProt A0A2K5TLN2 · UniProt P28472
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