Research workbench
Structure of alpha-1 glycine receptor by single particle electron cryo-microscopy, strychnine-bound state
Analyse Structure of alpha-1 glycine receptor by single particle electron… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JAD
- Type
- protein
- Length
- 1,685 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine receptor subunit ALPHAZ1
- Ligands
- SY9, NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 34% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Glycine receptor subunit ALPHAZ1 | protein | 337 | 34% helix, 31% strand | — |
Ligands and binding sites
- SY9 · Strychnine · ligand · 5 copies · chains A, E, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 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 | 1009 | 0.84 | 0.85 | 84 | empty |
| 2 | 878 | 0.80 | 0.83 | 112 | empty |
| 3 | 888 | 0.80 | 0.82 | 89 | SY9 |
| 4 | 451 | 0.76 | 0.84 | 48 | SY9 |
| 5 | 462 | 0.76 | 0.84 | 46 | SY9 |
Interfaces
5 interfaces between chains.
- D–E · 2251 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 2241 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2228 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 2191 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 2169 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3JAD · Structure of alpha-1 glycine receptor by single particle electron cryo-microscopy… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 3JAD · PDBe 3JAD
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