MolNFT v1 · #150716 · protein + RNA
Human nuclear RNA exosome exo-10-MPP6 complex
6H25 · Exosome complex component RRP45: “Human nuclear RNA exosome exo-10-MPP6 complex”. Electron microscopy, 20 pockets (best druggability 0.81). MolNFT v1 #150716 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6H25
- Type
- protein + RNA
- Length
- 2,977 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exosome complex component RRP45; Exosome complex component RRP41; Exosome complex…
- EC
- 3.1.13.-, 3.1.26.-
- UniProt
- Q06265, Q9NPD3, Q96B26, Q9NQT4, Q15024, Q5RKV6, Q9NQT5, Q13868, Q9Y3B2, Q9Y2L1, Q99547
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 12 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exosome complex component RRP45 | protein | 287 | 28% helix, 29% strand | Q06265 |
| B | Exosome complex component RRP41 | protein | 239 | 34% helix, 30% strand | Q9NPD3 |
| C | Exosome complex component RRP43 | protein | 264 | 28% helix, 33% strand | Q96B26 |
| D | Exosome complex component RRP46 | protein | 210 | 34% helix, 33% strand | Q9NQT4 |
| E | Exosome complex component RRP42 | protein | 287 | 27% helix, 26% strand | Q15024 |
| F | Exosome complex component MTR3 | protein | 244 | 29% helix, 30% strand | Q5RKV6 |
| G | Exosome complex component RRP40 | protein | 210 | 14% helix, 33% strand | Q9NQT5 |
| H | Exosome complex component RRP4 | protein | 275 | 21% helix, 27% strand | Q13868 |
| I | Exosome complex component CSL4 | protein | 50 | 0% helix, 52% strand | Q9Y3B2 |
| J | Exosome complex exonuclease RRP44 (EC 3.1.13.-, 3.1.26.-) | protein | 868 | 31% helix, 23% strand | Q9Y2L1 |
| K | M-phase phosphoprotein 6 | protein | 37 | 35% helix, 5% strand | Q99547 |
| R | U44 ssrna | rna | 6 | — | — |
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 | 874 | 0.81 | 0.83 | 90 | empty |
| 2 | 767 | 0.80 | 0.84 | 83 | empty |
| 3 | 953 | 0.80 | 0.82 | 77 | empty |
| 4 | 1001 | 0.78 | 0.80 | 105 | empty |
| 5 | 721 | 0.78 | 0.82 | 65 | empty |
Interfaces
19 interfaces between chains.
- C–F · 1847 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1638 Ų buried · 25 hydrogen bonds · protein-protein
- E–H · 1558 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 1426 Ų buried · 17 hydrogen bonds · protein-protein
- B–H · 1423 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6H25 · Human nuclear RNA exosome EXO-10-MPP6 complex · the same entry in another collection · chain R against R, TM-score 1.00
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 Q06265
- 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
- Every structure of UniProt Q9Y2L1
- Every structure of UniProt Q99547
- Elsewhere: RCSB PDB 6H25 · PDBe 6H25 · UniProt Q06265 · UniProt Q9NPD3 · UniProt Q96B26 · UniProt Q9NQT4 · UniProt Q15024 · UniProt Q5RKV6 · UniProt Q9NQT5 · UniProt Q13868 · UniProt Q9Y3B2 · UniProt Q9Y2L1 · UniProt Q99547
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