Research workbench
Crystal structure of human glycine receptor alpha-3 bound to strychnine
Analyse Crystal structure of human glycine receptor alpha-3 bound to strychnine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CFB
- Type
- protein
- Length
- 1,684 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine receptor subunit alpha-3,GLYCINE receptor subunit alpha-3
- UniProt
- O75311
- Ligands
- SY9, NAG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Glycine receptor subunit alpha-3,GLYCINE receptor subunit alpha-3 | protein | 339 | 34% helix, 29% strand | O75311 |
| C | Glycine receptor subunit alpha-3,GLYCINE receptor subunit alpha-3 | protein | 336 | 35% helix, 30% strand | O75311 |
| D | Glycine receptor subunit alpha-3,GLYCINE receptor subunit alpha-3 | protein | 331 | 36% helix, 32% strand | O75311 |
Ligands and binding sites
- SY9 · Strychnine · ligand · 5 copies · chains A, B, C, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains C, D, A, B, 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.83 | 0.84 | 97 | empty |
| 2 | 907 | 0.79 | 0.81 | 81 | SY9 |
| 3 | 884 | 0.78 | 0.81 | 91 | SY9 |
| 4 | 906 | 0.78 | 0.81 | 87 | SY9 |
| 5 | 486 | 0.72 | 0.81 | 45 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2316 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 2287 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 2285 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 2283 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 2268 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- O75311 · AlphaFold monomer V2.0 prediction for glycine receptor subunit alpha-3 (O75311) · a predicted model of the same protein · chain C against A, TM-score 0.90
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 O75311
- Elsewhere: RCSB PDB 5CFB · PDBe 5CFB · UniProt O75311
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