Research workbench
Crystal structure of the human RRP6 catalytic domain with D313N mutation in the active site
Analyse Crystal structure of the human RRP6 catalytic domain with D313N mutation in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SAF
- Type
- protein
- Length
- 761 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exosome component 10
- EC
- 3.1.13.-
- UniProt
- Q01780
- Ligands
- MG, YT3
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exosome component 10 (EC 3.1.13.-) | protein | 381 | 47% helix, 9% strand | Q01780 |
| B | Exosome component 10 (EC 3.1.13.-) | protein | 380 | 46% helix, 9% strand | Q01780 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- YT3 · Yttrium (III) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 809 | 0.78 | 0.82 | 81 | MG |
| 2 | 325 | 0.63 | 0.80 | 45 | empty |
| 3 | 227 | 0.58 | 0.79 | 29 | empty |
| 4 | 122 | 0.55 | 0.83 | 22 | empty |
| 5 | 171 | 0.48 | 0.77 | 31 | MG |
Interfaces
1 interface between chains.
- A–B · 853 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3SAF · Crystal structure of the human RRP6 catalytic domain with D313N mutation in the active… · the same entry in another collection · chain A against A, TM-score 1.00
- Q01780 · AlphaFold monomer V2.0 prediction for exosome component 10 (Q01780) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q01780
- Elsewhere: RCSB PDB 3SAF · PDBe 3SAF · UniProt Q01780
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