MolNFT v1 · #78485 · protein
Crystal structure of the human RRP6 catalytic domain with D313N mutation in the active site
3SAF · Exosome component 10: “Crystal structure of the human RRP6 catalytic domain with D313N mutation in the active site”. X-ray diffraction, 2 ligands (MG, YT3), 9 pockets (best druggability 0.78). MolNFT v1 #78485 on GenesisL1: 3D…
- 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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