Research workbench
Structure of a 9-subunit archaeal exosome bound to RNA
Analyse Structure of a 9-subunit archaeal exosome bound to RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JEA
- Type
- protein + RNA
- Length
- 720 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exosome complex exonuclease 2; Exosome complex exonuclease 1; RNA; Exosome complex…
- EC
- 3.1.13.-
- UniProt
- Q9UXC0, Q9UXC2, Q9UXC4
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exosome complex exonuclease 2 (EC 3.1.13.-) | protein | 274 | 28% helix, 36% strand | Q9UXC0 |
| B | Exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 234 | 31% helix, 33% strand | Q9UXC2 |
| C | RNA | rna | 5 | — | — |
| I | Exosome complex RNA-binding protein 1 | protein | 207 | 14% helix, 36% strand | Q9UXC4 |
Ligands and binding sites
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 751 | 0.75 | 0.80 | 69 | empty |
| 2 | 386 | 0.63 | 0.78 | 32 | empty |
| 3 | 121 | 0.53 | 0.82 | 19 | empty |
| 4 | 123 | 0.47 | 0.79 | 15 | empty |
| 5 | 51 | 0.41 | 0.82 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1922 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 538 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–C · 291 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–I · 269 Ų buried · 1 hydrogen bond · protein-protein
- B–I · 51 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2JEA · Structure of a 9-subunit archaeal exosome bound to RNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UXC2 · AlphaFold monomer V2.0 prediction for exosome complex component RRP41 (Q9UXC2) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q9UXC0 · AlphaFold monomer V2.0 prediction for exosome complex component RRP42 (Q9UXC0) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q9UXC4 · AlphaFold monomer V2.0 prediction for exosome complex component RRP4 (Q9UXC4) · a predicted model of the same protein · chain I against A, TM-score 0.85
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 Q9UXC0
- Every structure of UniProt Q9UXC2
- Every structure of UniProt Q9UXC4
- Elsewhere: RCSB PDB 2JEA · PDBe 2JEA · UniProt Q9UXC0 · UniProt Q9UXC2 · UniProt Q9UXC4
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