Research workbench
The structure of xendou: a splicing independent snorna processing endoribonuclease
Analyse The structure of xendou: a splicing independent snorna processing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C1W
- Type
- protein
- Length
- 820 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endou protein
- UniProt
- Q8JFY9
- Ligands
- PO4
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endou protein | protein | 273 | 36% helix, 22% strand | Q8JFY9 |
| B | Endou protein | protein | 276 | 34% helix, 22% strand | Q8JFY9 |
| C | Endou protein | protein | 271 | 35% helix, 22% strand | Q8JFY9 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 585 | 0.79 | 0.84 | 68 | PO4 |
| 2 | 1073 | 0.78 | 0.80 | 78 | PO4 |
| 3 | 116 | 0.58 | 0.85 | 28 | empty |
| 4 | 157 | 0.56 | 0.81 | 23 | empty |
| 5 | 84 | 0.37 | 0.76 | 25 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1098 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1093 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2C1W · The structure of XendoU: a splicing independent snoRNA processing endoribonuclease · the same entry in another collection · chain A against A, TM-score 1.00
- Q8JFY9 · AlphaFold monomer V2.0 prediction for POLY(U)-specific endoribonuclease-a (Q8JFY9) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 Q8JFY9
- Elsewhere: RCSB PDB 2C1W · PDBe 2C1W · UniProt Q8JFY9
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