Research workbench
The structure of methanothermobacter thermautotrophicus exosome core assembly
Analyse The structure of methanothermobacter thermautotrophicus exosome core assembly in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WNR
- Type
- protein
- Length
- 1,418 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable exosome complex exonuclease 2; Probable exosome complex exonuclease 1
- EC
- 3.1.13.-
- UniProt
- O26778, O26779
- Ligands
- PO4
- Pockets
- 13 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 29% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable exosome complex exonuclease 2 (EC 3.1.13.-) | protein | 261 | 30% helix, 38% strand | O26778 |
| B | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 222 | 30% helix, 33% strand | O26779 |
| C | Probable exosome complex exonuclease 2 (EC 3.1.13.-) | protein | 258 | 28% helix, 38% strand | O26778 |
| D | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 210 | 30% helix, 34% strand | O26779 |
| E | Probable exosome complex exonuclease 2 (EC 3.1.13.-) | protein | 250 | 27% helix, 38% strand | O26778 |
| F | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 217 | 30% helix, 31% strand | O26779 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 726 | 0.69 | 0.76 | 72 | empty |
| 2 | 645 | 0.66 | 0.76 | 68 | PO4 |
| 3 | 460 | 0.65 | 0.78 | 47 | empty |
| 4 | 412 | 0.61 | 0.77 | 47 | PO4 |
| 5 | 368 | 0.58 | 0.76 | 35 | PO4 |
Interfaces
6 interfaces between chains.
- A–B · 1416 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 1405 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1362 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1303 Ų buried · 18 hydrogen bonds · protein-protein
- C–F · 1302 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2WNR · The structure of Methanothermobacter thermautotrophicus exosome core assembly · the same entry in another collection · chain F against F, TM-score 1.00
- O26778 · AlphaFold monomer V2.0 prediction for exosome complex component RRP42 (O26778) · a predicted model of the same protein · chain E against A, TM-score 0.99
- O26779 · AlphaFold monomer V2.0 prediction for exosome complex component RRP41 (O26779) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 O26778
- Every structure of UniProt O26779
- Elsewhere: RCSB PDB 2WNR · PDBe 2WNR · UniProt O26778 · UniProt O26779
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