MolNFT v1 · #161461 · protein
Cryoem structure of a BETA3K279T GABA(A)R homomer in complex with histamine and megabody MB25
6QFA · Gamma-aminobutyric acid receptor subunit beta-3,GAMMA…: “Cryoem structure of a BETA3K279T GABA(A)R homomer in complex with histamine and megabody MB25”. Electron microscopy, 4 ligands (HSM, NAG, MAN), 20 pockets (best druggability…
- PDB
- 6QFA
- Type
- protein
- Length
- 2,270 residues
- Chains
- 10
- 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, B5Z8H1
- Ligands
- HSM, NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 28% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C, D, E, A | Gamma-aminobutyric acid receptor subunit beta-3,GAMMA- aminobutyric acid receptor subunit beta-3 | protein | 333 | 37% helix, 31% strand | P28472 |
| K, O, N, M, L | Outer membrane PROTEIN,OUTER membrane PROTEIN,OUTER membrane PROTEIN,OUTER membrane PROTEIN,UNCHARACTERIZED protein, uncharacterized PROTEIN,MB-C7HOPQ-NB25 | protein | 121 | 2% helix, 50% strand | B5Z8H1 |
Ligands and binding sites
- HSM · Histamine · ligand · 5 copies · chains B, A, C, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains B, K, L, C, M, D, N, E, O, A
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains B, K, L, C, M, D, N, E, O, A
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains B, C, D, E, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.83 | 0.83 | 103 | empty |
| 2 | 1000 | 0.82 | 0.83 | 113 | NAG |
| 3 | 400 | 0.74 | 0.84 | 60 | empty |
| 4 | 354 | 0.73 | 0.84 | 55 | empty |
| 5 | 332 | 0.72 | 0.84 | 41 | HSM |
Interfaces
15 interfaces between chains.
- B–A · 2763 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 2757 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 2757 Ų buried · 19 hydrogen bonds · protein-protein
- E–A · 2754 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 2750 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 6QFA · CryoEM structure of a beta3K279T GABA(A)R homomer in complex with histamine and megabody… · the same entry in another collection · chain A against A, 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 C 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 B5Z8H1
- Elsewhere: RCSB PDB 6QFA · PDBe 6QFA · UniProt P28472 · UniProt B5Z8H1
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