MolNFT v1 · #78584 · protein
Crystal structure of a paraspeckle-protein heterodimer, PSPC1/NONO
3SDE · Paraspeckle component 1: “Crystal structure of a paraspeckle-protein heterodimer, PSPC1/NONO”. X-ray diffraction, 4 pockets (best druggability 0.80). MolNFT v1 #78584 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3SDE
- Type
- protein
- Length
- 494 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Paraspeckle component 1; Non-pou domain-containing octamer-binding protein
- UniProt
- Q8WXF1, Q15233
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Paraspeckle component 1 | protein | 255 | 42% helix, 22% strand | Q8WXF1 |
| B | Non-pou domain-containing octamer-binding protein | protein | 239 | 40% helix, 25% strand | Q15233 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.80 | 0.81 | 86 | EDO |
| 2 | 189 | 0.46 | 0.74 | 30 | EDO |
| 3 | 83 | 0.35 | 0.75 | 17 | EDO |
| 4 | 78 | 0.30 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 4641 Ų buried · 75 hydrogen bonds · protein-protein
Compared structures
- 3SDE · Crystal structure of a paraspeckle-protein heterodimer, PSPC1/NONO · the same entry in another collection · chain A against A, TM-score 1.00
- Q8WXF1 · AlphaFold monomer V2.0 prediction for paraspeckle component 1 (Q8WXF1) · a predicted model of the same protein · chain A against A, TM-score 0.94
- Q15233 · AlphaFold monomer V2.0 prediction for non-pou domain-containing octamer-binding protein… · a predicted model of the same protein · chain B against A, TM-score 0.89
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 Q8WXF1
- Every structure of UniProt Q15233
- Elsewhere: RCSB PDB 3SDE · PDBe 3SDE · UniProt Q8WXF1 · UniProt Q15233
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.