Research workbench
The closed conformation of the sigma-1 receptor from xenopus laevis complexed with S1RA
Analyse The closed conformation of the sigma-1 receptor from xenopus laevis complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7W2D
- Type
- protein
- Length
- 2,565 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sigma non-opioid intracellular receptor 1
- UniProt
- Q6DCU6
- Ligands
- 88E, AU
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, B, F, H, I, L | Sigma non-opioid intracellular receptor 1 | protein | 215 | 42% helix, 28% strand | Q6DCU6 |
| C, D, K | Sigma non-opioid intracellular receptor 1 | protein | 216 | 39% helix, 28% strand | Q6DCU6 |
| G | Sigma non-opioid intracellular receptor 1 | protein | 204 | 39% helix, 30% strand | Q6DCU6 |
| J | Sigma non-opioid intracellular receptor 1 | protein | 208 | 38% helix, 29% strand | Q6DCU6 |
Ligands and binding sites
- 88E · 4-[2-(5-methyl-1-naphthalen-2-yl-pyrazol-3-yl) oxyethyl]morpholine · ligand · 12 copies · chains A, C, E, B, D, F, G, H, I, J, K, L
- AU · Gold ion · metal · 24 copies · chains A, C, I, E, B, D, F, G, H, J, K, L
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 | 250 | 0.85 | 0.96 | 36 | 88E |
| 2 | 226 | 0.85 | 0.97 | 36 | 88E |
| 3 | 228 | 0.84 | 0.96 | 36 | 88E |
| 4 | 232 | 0.84 | 0.96 | 37 | 88E |
| 5 | 240 | 0.84 | 0.96 | 38 | 88E |
Interfaces
24 interfaces between chains.
- G–H · 1021 Ų buried · 18 hydrogen bonds · protein-protein
- J–K · 1018 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1017 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1013 Ų buried · 17 hydrogen bonds · protein-protein
- H–I · 1002 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7W2D · The closed conformation of the sigma-1 receptor from Xenopus laevis complexed with S1RA · the same entry in another collection · chain L against L, 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
- Every structure of UniProt Q6DCU6
- Elsewhere: RCSB PDB 7W2D · PDBe 7W2D · UniProt Q6DCU6
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