MolNFT v1 · #189888 · protein
An open-like conformation of the sigma-1 receptor from xenopus laevis complexed with PRE084 by soaking
7W2G · Sigma non-opioid intracellular receptor 1: “An open-like conformation of the sigma-1 receptor from xenopus laevis complexed with PRE084 by soaking”. X-ray diffraction, 1 ligand (E84), 20 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 7W2G
- Type
- protein
- Length
- 2,564 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
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, I, L | Sigma non-opioid intracellular receptor 1 | protein | 214 | 43% helix, 29% strand | Q6DCU6 |
| B, E, G, J | Sigma non-opioid intracellular receptor 1 | protein | 213 | 42% helix, 29% strand | Q6DCU6 |
| C, F | Sigma non-opioid intracellular receptor 1 | protein | 216 | 44% helix, 29% strand | Q6DCU6 |
| H, K | Sigma non-opioid intracellular receptor 1 | protein | 212 | 42% helix, 29% strand | Q6DCU6 |
Ligands and binding sites
- E84 · 2-morpholin-4-ylethyl 1-phenylcyclohexane-1-carboxylate · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- BOG · octyl beta-D-glucopyranoside · additive · 7 copies · chains A, B, D, E, G, I, H, J, L, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 256 | 0.81 | 0.92 | 36 | E84 |
| 2 | 265 | 0.80 | 0.92 | 41 | E84 |
| 3 | 286 | 0.80 | 0.91 | 40 | E84 |
| 4 | 283 | 0.80 | 0.91 | 40 | E84 |
| 5 | 296 | 0.79 | 0.90 | 41 | E84 |
Interfaces
23 interfaces between chains.
- B–C · 999 Ų buried · 14 hydrogen bonds · protein-protein
- K–L · 999 Ų buried · 16 hydrogen bonds · protein-protein
- H–I · 999 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 997 Ų buried · 13 hydrogen bonds · protein-protein
- G–I · 996 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 7W2G · An open-like conformation of the sigma-1 receptor from Xenopus laevis complexed with… · 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 7W2G · PDBe 7W2G · UniProt Q6DCU6
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