Research workbench
Crystal structure of the sigma-1 receptor from Xenopus laevis with side opening
Analyse Crystal structure of the sigma-1 receptor from Xenopus laevis with side opening in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8YBB
- Type
- protein
- Length
- 1,336 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.12
- Source
- Xenopus laevis
- Molecule
- Sigma non-opioid intracellular receptor 1
- UniProt
- Q6DCU6
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · resolution 3.12 · 2 distinct chains · 43% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sigma non-opioid intracellular receptor 1 | protein | 221 | 44% helix, 28% strand | Q6DCU6 |
| B, C, D, E, F | Sigma non-opioid intracellular receptor 1 | protein | 223 | 43% helix, 28% strand | Q6DCU6 |
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.84 | 0.96 | 37 | empty |
| 2 | 287 | 0.83 | 0.94 | 40 | empty |
| 3 | 284 | 0.83 | 0.93 | 40 | empty |
| 4 | 953 | 0.78 | 0.80 | 99 | empty |
| 5 | 914 | 0.78 | 0.80 | 98 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1625 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1617 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 1610 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1603 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 1595 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- Q6DCU6 · AlphaFold monomer V2.0 prediction for sigma non-opioid intracellular receptor 1 (Q6DCU6) · a predicted model of the same protein · chain B against A, TM-score 0.87
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 Q6DCU6
- Elsewhere: RCSB PDB 8YBB · PDBe 8YBB · UniProt Q6DCU6
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