MolNFT v1 · #119574 · protein
Cryo-EM structure of yeast cytoplasmic exosome
5G06 · Exosome complex component RRP45: “Cryo-EM structure of yeast cytoplasmic exosome”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #119574 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5G06
- Type
- protein
- Length
- 3,420 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exosome complex component RRP45; Exosome complex component SKI6; Exosome complex…
- EC
- 3.1.13.1
- UniProt
- Q05636, P46948, P25359, P53256, Q12277, P48240, Q08285, P38792, P53859, Q08162, Q08491
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 11 distinct chains · 27% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exosome complex component RRP45 | protein | 302 | 30% helix, 29% strand | Q05636 |
| B | Exosome complex component SKI6 | protein | 240 | 29% helix, 30% strand | P46948 |
| C | Exosome complex component RRP43 | protein | 335 | 26% helix, 30% strand | P25359 |
| D | Exosome complex component RRP46 | protein | 223 | 34% helix, 37% strand | P53256 |
| E | Exosome complex component RRP42 | protein | 265 | 24% helix, 33% strand | Q12277 |
| F | Exosome complex component MTR3 | protein | 211 | 27% helix, 31% strand | P48240 |
| G | Exosome complex component RRP40 | protein | 236 | 19% helix, 28% strand | Q08285 |
| H | Exosome complex component RRP4 | protein | 293 | 23% helix, 25% strand | P38792 |
| I | Exosome complex component CSL4 | protein | 227 | 4% helix, 47% strand | P53859 |
| J | Exosome complex exonuclease DIS3 (EC 3.1.13.1) | protein | 993 | 31% helix, 23% strand | Q08162 |
| P | Superkiller protein 7 | protein | 95 | 60% helix, 0% strand | Q08491 |
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 | 1009 | 0.84 | 0.85 | 93 | empty |
| 2 | 1166 | 0.84 | 0.85 | 105 | empty |
| 3 | 199 | 0.82 | 0.95 | 37 | empty |
| 4 | 947 | 0.81 | 0.83 | 74 | empty |
| 5 | 662 | 0.79 | 0.84 | 56 | empty |
Interfaces
31 interfaces between chains.
- C–F · 2097 Ų buried · 18 hydrogen bonds · protein-protein
- B–J · 1947 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1917 Ų buried · 17 hydrogen bonds · protein-protein
- E–H · 1904 Ų buried · 17 hydrogen bonds · protein-protein
- F–I · 1557 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
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 Q05636
- Every structure of UniProt P46948
- Every structure of UniProt P25359
- Every structure of UniProt P53256
- Every structure of UniProt Q12277
- Every structure of UniProt P48240
- Every structure of UniProt Q08285
- Every structure of UniProt P38792
- Every structure of UniProt P53859
- Every structure of UniProt Q08162
- Every structure of UniProt Q08491
- Elsewhere: RCSB PDB 5G06 · PDBe 5G06 · UniProt Q05636 · UniProt P46948 · UniProt P25359 · UniProt P53256 · UniProt Q12277 · UniProt P48240 · UniProt Q08285 · UniProt P38792 · UniProt P53859 · UniProt Q08162 · UniProt Q08491
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