Research workbench
Full length ALPHA1 glycine receptor in presence of 0.1MM glycine and 32UM tetrahydrocannabinol
Analyse Full length ALPHA1 glycine receptor in presence of 0.1MM glycine and 32UM… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M6O
- Type
- protein
- Length
- 1,785 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine receptor subunit ALPHAZ1
- UniProt
- O93430
- Ligands
- TCI, GLY, NAG
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 1 distinct chain · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Glycine receptor subunit ALPHAZ1 | protein | 357 | 36% helix, 25% strand | O93430 |
Ligands and binding sites
- TCI · (6aR,10aR)-6,6,9-trimethyl-3-pentyl-6a,7,8,10a-tetrahydro-6H-benzo[c]chromen-1-ol · ligand · 5 copies · chains A, B, C, D, E
- GLY · Glycine · ligand · 5 copies · chains A, E, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B, C, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 920 | 0.78 | 0.80 | 53 | empty |
| 2 | 1054 | 0.77 | 0.79 | 104 | GLY |
| 3 | 1002 | 0.77 | 0.79 | 106 | GLY |
| 4 | 1038 | 0.76 | 0.78 | 109 | empty |
| 5 | 98 | 0.72 | 0.94 | 26 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2210 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 2209 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 2209 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 2181 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 2120 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 7M6O · Full length alpha1 Glycine receptor in presence of 0.1mM Glycine and 32uM… · the same entry in another collection · chain D against D, TM-score 1.00
- O93430 · AlphaFold monomer V2.0 prediction for glycine receptor subunit ALPHAZ1 (O93430) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 O93430
- Elsewhere: RCSB PDB 7M6O · PDBe 7M6O · UniProt O93430
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