Research workbench
Cryoem structure of zebra fish alpha-1 glycine receptor ygf mutant bound with GABA in sma, desensitized state
Analyse Cryoem structure of zebra fish alpha-1 glycine receptor ygf mutant bound with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PLP
- Type
- protein
- Length
- 1,730 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine receptor subunit ALPHAZ1
- UniProt
- O93430
- Ligands
- ABU, NAG, BMA
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 1 distinct chain · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Glycine receptor subunit ALPHAZ1 | protein | 346 | 34% helix, 25% strand | O93430 |
Ligands and binding sites
- ABU · Gamma-amino-butanoic acid · ligand · 5 copies · chains A, B, C, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, C, D, E
- BMA · beta-D-mannopyranose · sugar · 5 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.80 | 0.82 | 75 | empty |
| 2 | 517 | 0.73 | 0.82 | 70 | empty |
| 3 | 605 | 0.73 | 0.80 | 73 | empty |
| 4 | 588 | 0.73 | 0.80 | 75 | empty |
| 5 | 470 | 0.72 | 0.82 | 64 | empty |
Interfaces
5 interfaces between chains.
- D–E · 2587 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 2581 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2580 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 2576 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2572 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6PLP · CryoEM structure of zebra fish alpha-1 glycine receptor YGF mutant bound with GABA in… · the same entry in another collection · chain A against A, TM-score 1.00
- O93430 · AlphaFold monomer V2.0 prediction for glycine receptor subunit ALPHAZ1 (O93430) · a predicted model of the same protein · chain E 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 O93430
- Elsewhere: RCSB PDB 6PLP · PDBe 6PLP · UniProt O93430
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.