Research workbench
Structure of the RRP6-RRP47 interaction
Analyse Structure of the RRP6-RRP47 interaction in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WFC
- Type
- protein
- Length
- 567 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exosome complex exonuclease RRP6; Exosome complex protein LRP1
- EC
- 3.1.13.-
- UniProt
- Q12149, P38801
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 6 distinct chains · 86% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exosome complex exonuclease RRP6 (EC 3.1.13.-) | protein | 95 | 84% helix, 0% strand | Q12149 |
| B | Exosome complex protein LRP1 | protein | 118 | 86% helix, 0% strand | P38801 |
| C | Exosome complex exonuclease RRP6 (EC 3.1.13.-) | protein | 93 | 87% helix, 0% strand | Q12149 |
| D | Exosome complex protein LRP1 | protein | 98 | 83% helix, 0% strand | P38801 |
| E | Exosome complex exonuclease RRP6 (EC 3.1.13.-) | protein | 70 | 91% helix, 0% strand | Q12149 |
| F | Exosome complex protein LRP1 | protein | 93 | 85% helix, 0% strand | P38801 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.65 | 0.79 | 51 | empty |
| 2 | 133 | 0.58 | 0.83 | 28 | empty |
| 3 | 126 | 0.40 | 0.75 | 23 | empty |
| 4 | 104 | 0.36 | 0.74 | 20 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2920 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2906 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 2084 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 908 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 45 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4WFC · Structure of the Rrp6-Rrp47 interaction · the same entry in another collection · chain F against F, TM-score 1.00
- P38801 · AlphaFold monomer V2.0 prediction for exosome complex protein LRP1 (P38801) · a predicted model of the same protein · chain F against A, TM-score 0.98
- Q12149 · AlphaFold monomer V2.0 prediction for exosome complex exonuclease RRP6 (Q12149) · a predicted model of the same protein · chain C against A, TM-score 0.86
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
- Every structure of UniProt P38801
- Elsewhere: RCSB PDB 4WFC · PDBe 4WFC · UniProt Q12149 · UniProt P38801
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