MolNFT v1 · #185967 · protein
Cryo-EM structure of human full-length extrasynaptic ALPHA4BETA3DELTA GABA(A)R in complex with thip (gaboxadol), histamine and nanobody NB25
7QNC · Gamma-aminobutyric acid receptor subunit alpha-4: “Cryo-EM structure of human full-length extrasynaptic ALPHA4BETA3DELTA GABA(A)R in complex with thip…”. Electron microscopy, 6 ligands (D10, EI7, HSM), 20 pockets (best druggability…
- PDB
- 7QNC
- Type
- protein
- Length
- 1,881 residues
- Chains
- 7
- 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, O14764
- Ligands
- D10, EI7, HSM, NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 34% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma-aminobutyric acid receptor subunit alpha-4 | protein | 335 | 38% helix, 31% strand | P48169 |
| B, C, D | Gamma-aminobutyric acid receptor subunit beta-3 | protein | 327 | 38% helix, 32% strand | P28472 |
| E | Gamma-aminobutyric acid receptor subunit delta | protein | 323 | 36% helix, 29% strand | O14764 |
| F, G | Nanobody NB25 | protein | 121 | 5% helix, 52% strand | — |
Ligands and binding sites
- D10 · Decane · ligand · 3 copies · chains B, C, D
- EI7 · 4,5,6,7-tetrahydro-[1,2]oxazolo[5,4-c]pyridin-3-one · ligand · 2 copies · chains A, B, D, E
- HSM · Histamine · ligand · 2 copies · chains B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B, C, F, D, G, E
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains C, B, F, D, G
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1182 | 0.82 | 0.83 | 119 | empty |
| 2 | 609 | 0.78 | 0.84 | 77 | empty |
| 3 | 276 | 0.75 | 0.88 | 44 | empty |
| 4 | 610 | 0.75 | 0.82 | 58 | NAG |
| 5 | 527 | 0.74 | 0.82 | 59 | empty |
Interfaces
9 interfaces between chains.
- C–D · 2798 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 2739 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 2731 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2674 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 2480 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 glycan, 7 disulfide (N-glycosylation, disulfide).
Compared structures
- 7QNC · Cryo-EM structure of human full-length extrasynaptic alpha4beta3delta GABA(A)R 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
- 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 0.98
- O14764 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor subunit delta… · a predicted model of the same protein · chain E against A, TM-score 0.97
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 O14764
- Elsewhere: RCSB PDB 7QNC · PDBe 7QNC · UniProt P48169 · UniProt P28472 · UniProt O14764
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