Research workbench
Crystal structure of the P. abyssi exosome RNase pH ring complexed with a single stranded 10-mer POLY(A) RNA
Analyse Crystal structure of the P. abyssi exosome RNase pH ring complexed with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PO1
- Type
- protein + RNA
- Length
- 510 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 10-mer POLY(A); Probable exosome complex exonuclease 1; Probable exosome complex…
- EC
- 3.1.13.-
- UniProt
- Q9V119, Q9V118
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 10-mer POLY(A) | rna | 7 | — | — |
| A | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 236 | 35% helix, 31% strand | Q9V119 |
| B | Probable exosome complex exonuclease 2 (EC 3.1.13.-) | protein | 267 | 31% helix, 34% strand | Q9V118 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.54 | 0.82 | 22 | empty |
| 2 | 124 | 0.49 | 0.79 | 16 | MPD |
| 3 | 65 | 0.30 | 0.75 | 13 | empty |
| 4 | 56 | 0.28 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1245 Ų buried · 27 hydrogen bonds · protein-protein
- C–A · 531 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–B · 16 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 2PO1 · Crystal structure of the P. abyssi exosome RNase PH ring complexed with a single stranded… · the same entry in another collection · chain C against C, TM-score 1.00
- Q9V119 · AlphaFold monomer V2.0 prediction for exosome complex component RRP41 (Q9V119) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9V118 · AlphaFold monomer V2.0 prediction for exosome complex component RRP42 (Q9V118) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q9V119
- Every structure of UniProt Q9V118
- Elsewhere: RCSB PDB 2PO1 · PDBe 2PO1 · UniProt Q9V119 · UniProt Q9V118
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.