MolNFT v1 · #114813 · protein + RNA
Crystal structure of the RRP6 catalytic domain bound to POLY(U) RNA
5C0Y · Exosome complex exonuclease RRP6: “Crystal structure of the RRP6 catalytic domain bound to POLY(U) RNA”. X-ray diffraction, 1 ligand (MG), 12 pockets (best druggability 0.79). MolNFT v1 #114813 on GenesisL1: 3D structure, binding…
- PDB
- 5C0Y
- Type
- protein + RNA
- Length
- 782 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exosome complex exonuclease RRP6; Poly U RNA
- EC
- 3.1.13.-
- UniProt
- Q12149
- Ligands
- MG
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exosome complex exonuclease RRP6 (EC 3.1.13.-) | protein | 386 | 45% helix, 10% strand | Q12149 |
| B | Exosome complex exonuclease RRP6 (EC 3.1.13.-) | protein | 388 | 46% helix, 10% strand | Q12149 |
| D | Poly U RNA | rna | 6 | — | — |
| C | Poly U RNA | rna | 2 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.79 | 0.81 | 89 | empty |
| 2 | 454 | 0.62 | 0.76 | 40 | empty |
| 3 | 239 | 0.60 | 0.80 | 35 | empty |
| 4 | 263 | 0.59 | 0.79 | 39 | empty |
| 5 | 188 | 0.51 | 0.77 | 27 | empty |
Interfaces
4 interfaces between chains.
- B–D · 810 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–B · 688 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 204 Ų buried · 1 hydrogen bond · protein-nucleic
- A–D · 106 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 5C0Y · Crystal structure of the Rrp6 catalytic domain bound to poly(U) RNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q12149 · AlphaFold monomer V2.0 prediction for exosome complex exonuclease RRP6 (Q12149) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q12149
- Elsewhere: RCSB PDB 5C0Y · PDBe 5C0Y · UniProt Q12149
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