MolNFT v1 · #114812 · protein + RNA
Structure of a 12-subunit nuclear exosome complex bound to structured RNA
5C0X · Exosome complex component RRP45: “Structure of a 12-subunit nuclear exosome complex bound to structured RNA”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.83). MolNFT v1 #114812 on GenesisL1: 3D structure…
- PDB
- 5C0X
- Type
- protein + RNA
- Length
- 3,664 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exosome complex component RRP45; Exosome complex component SKI6; Exosome complex…
- EC
- 3.1.13.-, 3.1.26.-
- UniProt
- Q05636, P46948, P25359, P53256, Q12277, P48240, Q08285, P38792, P53859, Q08162, Q12149
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 12 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exosome complex component RRP45 | protein | 299 | 34% helix, 29% strand | Q05636 |
| B | Exosome complex component SKI6 | protein | 244 | 30% helix, 29% strand | P46948 |
| C | Exosome complex component RRP43 | protein | 339 | 25% helix, 36% strand | P25359 |
| D | Exosome complex component RRP46 | protein | 223 | 33% helix, 35% strand | P53256 |
| E | Exosome complex component RRP42 | protein | 267 | 26% helix, 32% strand | Q12277 |
| F | Exosome complex component MTR3 | protein | 215 | 30% helix, 34% strand | P48240 |
| G | Exosome complex component RRP40 | protein | 237 | 19% helix, 30% strand | Q08285 |
| H | Exosome complex component RRP4 | protein | 293 | 24% helix, 29% strand | P38792 |
| I | Exosome complex component CSL4 | protein | 222 | 3% helix, 49% strand | P53859 |
| J | Exosome complex exonuclease DIS3 (EC 3.1.13.-, 3.1.26.-) | protein | 944 | 32% helix, 26% strand | Q08162 |
| K | Exosome complex exonuclease RRP6 (EC 3.1.13.-) | protein | 350 | 42% helix, 11% strand | Q12149 |
| R | RNA synthetic | rna | 31 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.83 | 0.84 | 115 | empty |
| 2 | 892 | 0.83 | 0.85 | 106 | empty |
| 3 | 887 | 0.82 | 0.84 | 92 | empty |
| 4 | 798 | 0.82 | 0.85 | 77 | empty |
| 5 | 811 | 0.80 | 0.83 | 99 | empty |
Interfaces
40 interfaces between chains.
- C–F · 1987 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1893 Ų buried · 35 hydrogen bonds · protein-protein
- E–H · 1776 Ų buried · 30 hydrogen bonds · protein-protein
- C–K · 1591 Ų buried · 17 hydrogen bonds · protein-protein
- D–G · 1436 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- P53256 · AlphaFold monomer V2.0 prediction for exosome complex component RRP46 (P53256) · a predicted model of the same protein · chain D against A, TM-score 0.99
- Q12277 · AlphaFold monomer V2.0 prediction for exosome complex component RRP42 (Q12277) · a predicted model of the same protein · chain E against A, TM-score 0.99
- P25359 · AlphaFold monomer V2.0 prediction for exosome complex component RRP43 (P25359) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P48240 · AlphaFold monomer V2.0 prediction for exosome complex component MTR3 (P48240) · a predicted model of the same protein · chain F against A, TM-score 0.97
- P46948 · AlphaFold monomer V2.0 prediction for exosome complex component SKI6 (P46948) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q08285 · AlphaFold monomer V2.0 prediction for exosome complex component RRP40 (Q08285) · a predicted model of the same protein · chain G against A, TM-score 0.96
- Q05636 · AlphaFold monomer V2.0 prediction for exosome complex component RRP45 (Q05636) · a predicted model of the same protein · chain A against A, TM-score 0.95
- P38792 · AlphaFold monomer V2.0 prediction for exosome complex component RRP4 (P38792) · a predicted model of the same protein · chain H against A, TM-score 0.92
- Q08162 · AlphaFold monomer V2.0 prediction for exosome complex exonuclease DIS3 (Q08162) · a predicted model of the same protein · chain J against A, TM-score 0.90
- Q12149 · AlphaFold monomer V2.0 prediction for exosome complex exonuclease RRP6 (Q12149) · a predicted model of the same protein · chain K against A, TM-score 0.77
- P53859 · AlphaFold monomer V2.0 prediction for exosome complex component CSL4 (P53859) · a predicted model of the same protein · chain I against A, TM-score 0.74
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 Q05636
- Every structure of UniProt P46948
- Every structure of UniProt P25359
- Every structure of UniProt P53256
- Every structure of UniProt Q12277
- Every structure of UniProt P48240
- Every structure of UniProt Q08285
- Every structure of UniProt P38792
- Every structure of UniProt P53859
- Every structure of UniProt Q08162
- Every structure of UniProt Q12149
- Elsewhere: RCSB PDB 5C0X · PDBe 5C0X · UniProt Q05636 · UniProt P46948 · UniProt P25359 · UniProt P53256 · UniProt Q12277 · UniProt P48240 · UniProt Q08285 · UniProt P38792 · UniProt P53859 · UniProt Q08162 · UniProt Q12149
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