MolNFT v1 · #108707 · protein
Structure of the RRP6-RRP47-MTR4 interaction
4WFD · Exosome complex exonuclease RRP6: “Structure of the RRP6-RRP47-MTR4 interaction”. X-ray diffraction, 1 ligand (YT3), 7 pockets (best druggability 0.58). MolNFT v1 #108707 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4WFD
- Type
- protein
- Length
- 582 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exosome complex exonuclease RRP6; Exosome complex protein LRP1; ATP-dependent RNA…
- EC
- 3.1.13.-, 3.6.4.13
- UniProt
- Q12149, P38801, P47047
- Ligands
- YT3
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 8 distinct chains · 83% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exosome complex exonuclease RRP6 (EC 3.1.13.-) | protein | 91 | 88% helix, 0% strand | Q12149 |
| B | Exosome complex protein LRP1 | protein | 100 | 80% helix, 0% strand | P38801 |
| C | ATP-dependent RNA helicase DOB1 (EC 3.6.4.13) | protein | 14 | 29% helix, 0% strand | P47047 |
| D | Exosome complex exonuclease RRP6 (EC 3.1.13.-) | protein | 85 | 88% helix, 0% strand | Q12149 |
| E | Exosome complex protein LRP1 | protein | 101 | 83% helix, 0% strand | P38801 |
| F, I | ATP-dependent RNA helicase DOB1 (EC 3.6.4.13) | protein | 8 | 50% helix, 0% strand | P47047 |
| G | Exosome complex exonuclease RRP6 (EC 3.1.13.-) | protein | 82 | 90% helix, 0% strand | Q12149 |
| H | Exosome complex protein LRP1 | protein | 93 | 80% helix, 0% strand | P38801 |
Ligands and binding sites
- YT3 · Yttrium (III) ion · metal · 22 copies · chains A, B, C, D, E, F, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.58 | 0.89 | 20 | empty |
| 2 | 77 | 0.38 | 0.77 | 14 | empty |
| 3 | 77 | 0.36 | 0.76 | 17 | empty |
| 4 | 76 | 0.36 | 0.76 | 15 | empty |
| 5 | 56 | 0.36 | 0.79 | 16 | empty |
Interfaces
12 interfaces between chains.
- A–B · 2909 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 2805 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 2674 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 447 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 370 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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
- Every structure of UniProt P47047
- Elsewhere: RCSB PDB 4WFD · PDBe 4WFD · UniProt Q12149 · UniProt P38801 · UniProt P47047
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