MolNFT v1 · #45855 · protein
Structure of the human RNA exosome composed of RRP41, RRP45, RRP46, RRP43, MTR3, RRP42, CSL4, RRP4, and RRP40
2NN6 · POLYMYOSITIS/SCLERODERMA autoantigen 1: “Structure of the human RNA exosome composed of RRP41, RRP45, RRP46, RRP43, MTR3, RRP42, CSL4, RRP4, and RRP40”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #45855 on…
- 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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