MolNFT v2 · #186585 · protein
Full length alpha1 Glycine receptor in presence of 0.1mM Glycine and 32uM Tetrahydrocannabinol
7M6O · Glycine receptor subunit alphaZ1: “Full length alpha1 Glycine receptor in presence of 0.1mM Glycine and 32uM Tetrahydrocannabinol”. Electron microscopy at 2.84, 3 ligands (TCI, GLY, NAG), 20 pockets (best druggability 0.78). MolNFT…
- PDB
- 7M6O
- Type
- protein
- Length
- 1,785 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.84
- Source
- Danio rerio
- Molecule
- Glycine receptor subunit alphaZ1
- UniProt
- O93430
- Ligands
- TCI, GLY, NAG
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · resolution 2.84 · 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 E against E, 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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