Research workbench
Full length ALPHA1 glycine receptor in presence of 32UM tetrahydrocannabinol
Analyse Full length ALPHA1 glycine receptor in presence of 32UM tetrahydrocannabinol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M6M
- Type
- protein
- Length
- 1,720 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine receptor subunit ALPHAZ1
- UniProt
- O93430
- Ligands
- TCI, NAG
- Pockets
- 14 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 34% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, D | Glycine receptor subunit ALPHAZ1 | protein | 344 | 34% helix, 31% 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, E, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, C, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.85 | 0.86 | 97 | empty |
| 2 | 1007 | 0.80 | 0.82 | 95 | empty |
| 3 | 481 | 0.75 | 0.83 | 53 | empty |
| 4 | 469 | 0.74 | 0.83 | 51 | empty |
| 5 | 477 | 0.74 | 0.83 | 52 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2596 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 2595 Ų buried · 18 hydrogen bonds · protein-protein
- E–D · 2579 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2559 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2531 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan (N-glycosylation).
Compared structures
- 7M6M · Full length alpha1 Glycine receptor in presence of 32uM Tetrahydrocannabinol · 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 0.92
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 7M6M · PDBe 7M6M · UniProt O93430
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