MolNFT v1 · #142594 · protein
Cryo-EM structure of the human ALPHA5BETA3 gabaa receptor in complex with GABA and NB25
6A96: “Cryo-EM structure of the human ALPHA5BETA3 gabaa receptor in complex with GABA and NB25”. Electron microscopy, 4 ligands (ABU, NAG, MAN), 20 pockets (best druggability 0.84). MolNFT v1 #142594 on GenesisL1: 3D structure, binding…
- PDB
- 6A96
- Type
- protein
- Length
- 2,043 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NB25; Gamma-aminobutyric acid receptor subunit beta-3,GAMMA- aminobutyric acid receptor…
- UniProt
- P28472, P31644
- Ligands
- ABU, NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K, O | NB25 | protein | 125 | 7% helix, 35% strand | — |
| L | NB25 | protein | 124 | 5% helix, 31% strand | — |
| B, E, C, D | Gamma-aminobutyric acid receptor subunit beta-3,GAMMA- aminobutyric acid receptor subunit beta-3 | protein | 333 | 34% helix, 28% strand | P28472 |
| A | Gamma-aminobutyric acid receptor subunit alpha-5,GAMMA- aminobutyric acid receptor subunit alpha-5 | protein | 337 | 31% helix, 25% strand | P31644 |
Ligands and binding sites
- ABU · Gamma-amino-butanoic acid · ligand · chains B, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains B, A, O, E, L, C, K, D
- MAN · alpha-D-mannopyranose · sugar · 14 copies · chains B, D, E, O, C, L, K
- BMA · beta-D-mannopyranose · sugar · 9 copies · chains B, E, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 817 | 0.84 | 0.86 | 94 | empty |
| 2 | 666 | 0.82 | 0.86 | 77 | empty |
| 3 | 696 | 0.82 | 0.85 | 75 | empty |
| 4 | 407 | 0.80 | 0.88 | 54 | empty |
| 5 | 340 | 0.78 | 0.88 | 53 | empty |
Interfaces
11 interfaces between chains.
- B–A · 2505 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 2347 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 2163 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 2059 Ų buried · 9 hydrogen bonds · protein-protein
- E–D · 1972 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 glycan, 9 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 6A96 · Cryo-EM structure of the human alpha5beta3 GABAA receptor in complex with GABA and Nb25 · the same entry in another collection · chain D against D, 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 0.97
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 P28472
- Every structure of UniProt P31644
- Elsewhere: RCSB PDB 6A96 · PDBe 6A96 · UniProt P28472 · UniProt P31644
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.