Research workbench
The closed conformation of the sigma-1 receptor from xenopus laevis complexed with PRE084
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
- 7W2C
- Type
- protein
- Length
- 2,590 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
- E84, AU
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, B, F, H, I, K, L | Sigma non-opioid intracellular receptor 1 | protein | 215 | 41% helix, 28% strand | Q6DCU6 |
| C | Sigma non-opioid intracellular receptor 1 | protein | 217 | 39% helix, 28% strand | Q6DCU6 |
| D | Sigma non-opioid intracellular receptor 1 | protein | 219 | 41% helix, 26% strand | Q6DCU6 |
| G | Sigma non-opioid intracellular receptor 1 | protein | 214 | 39% helix, 28% strand | Q6DCU6 |
| J | Sigma non-opioid intracellular receptor 1 | protein | 220 | 40% helix, 26% strand | Q6DCU6 |
Ligands and binding sites
- E84 · 2-morpholin-4-ylethyl 1-phenylcyclohexane-1-carboxylate · 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, E, B, D, I, F, G, H, J, K, L
- BOG · octyl beta-D-glucopyranoside · additive · 3 copies · chains A, E, C, B, D, H, J, 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 | 276 | 0.85 | 0.96 | 39 | E84 |
| 2 | 273 | 0.85 | 0.96 | 35 | E84 |
| 3 | 268 | 0.85 | 0.96 | 36 | E84 |
| 4 | 274 | 0.85 | 0.96 | 36 | E84 |
| 5 | 265 | 0.85 | 0.96 | 36 | E84 |
Interfaces
24 interfaces between chains.
- J–K · 1029 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1026 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 1025 Ų buried · 15 hydrogen bonds · protein-protein
- G–I · 1019 Ų buried · 19 hydrogen bonds · protein-protein
- J–L · 1019 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7W2C · The closed conformation of the sigma-1 receptor from Xenopus laevis complexed with PRE084 · 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 7W2C · PDBe 7W2C · UniProt Q6DCU6
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