Research workbench
Structure of the human RNA exosome composed of RRP41, RRP45, RRP46, RRP43, MTR3, RRP42, CSL4, RRP4, and RRP40
Analyse Structure of the human RNA exosome composed of RRP41, RRP45, RRP46, RRP43… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NN6
- Type
- protein
- Length
- 2,214 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POLYMYOSITIS/SCLERODERMA autoantigen 1; Exosome complex exonuclease RRP41; Exosome…
- EC
- 3.1.13.-
- UniProt
- Q86Y41, Q9NPD3, Q96B26, Q9NQT4, Q15024, Q5RKV6, Q9NQT5, Q13868, Q9Y3B2
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 9 distinct chains · 25% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POLYMYOSITIS/SCLERODERMA autoantigen 1 | protein | 340 | 33% helix, 21% strand | Q86Y41 |
| B | Exosome complex exonuclease RRP41 (EC 3.1.13.-) | protein | 235 | 29% helix, 29% strand | Q9NPD3 |
| C | Exosome complex exonuclease RRP43 (EC 3.1.13.-) | protein | 270 | 24% helix, 23% strand | Q96B26 |
| D | Exosome complex exonuclease RRP46 (EC 3.1.13.-) | protein | 205 | 34% helix, 33% strand | Q9NQT4 |
| E | Exosome complex exonuclease RRP42 (EC 3.1.13.-) | protein | 275 | 27% helix, 20% strand | Q15024 |
| F | Exosome component 6 | protein | 223 | 29% helix, 24% strand | Q5RKV6 |
| G | Exosome complex exonuclease RRP40 (EC 3.1.13.-) | protein | 236 | 16% helix, 27% strand | Q9NQT5 |
| H | Exosome complex exonuclease RRP4 (EC 3.1.13.-) | protein | 250 | 22% helix, 27% strand | Q13868 |
| I | 3'-5' exoribonuclease CSL4 homolog (EC 3.1.13.-) | protein | 180 | 3% helix, 34% strand | Q9Y3B2 |
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 | 1048 | 0.81 | 0.82 | 131 | empty |
| 2 | 171 | 0.81 | 0.96 | 43 | empty |
| 3 | 1051 | 0.80 | 0.81 | 93 | empty |
| 4 | 996 | 0.79 | 0.81 | 101 | empty |
| 5 | 130 | 0.79 | 0.96 | 38 | empty |
Interfaces
17 interfaces between chains.
- A–D · 2081 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 1337 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1312 Ų buried · 23 hydrogen bonds · protein-protein
- B–H · 1202 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 1140 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 2NN6 · Structure of the human RNA exosome composed of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42… · the same entry in another collection · chain I against I, TM-score 1.00
- Q9NPD3 · AlphaFold monomer V2.0 prediction for exosome complex component RRP41 (Q9NPD3) · a predicted model of the same protein · chain B against A, TM-score 0.96
- Q9NQT4 · AlphaFold monomer V2.0 prediction for exosome complex component RRP46 (Q9NQT4) · a predicted model of the same protein · chain D against A, TM-score 0.96
- Q96B26 · AlphaFold monomer V2.0 prediction for exosome complex component RRP43 (Q96B26) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 Q86Y41
- Every structure of UniProt Q9NPD3
- Every structure of UniProt Q96B26
- Every structure of UniProt Q9NQT4
- Every structure of UniProt Q15024
- Every structure of UniProt Q5RKV6
- Every structure of UniProt Q9NQT5
- Every structure of UniProt Q13868
- Every structure of UniProt Q9Y3B2
- Elsewhere: RCSB PDB 2NN6 · PDBe 2NN6 · UniProt Q86Y41 · UniProt Q9NPD3 · UniProt Q96B26 · UniProt Q9NQT4 · UniProt Q15024 · UniProt Q5RKV6 · UniProt Q9NQT5 · UniProt Q13868 · UniProt Q9Y3B2
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