MolNFT v1 · #70021 · protein
Crystal structure of the S. solfataricus archaeal exosome
3L7Z · Probable exosome complex exonuclease 2: “Crystal structure of the S. solfataricus archaeal exosome”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.79). MolNFT v1 #70021 on GenesisL1: 3D structure, binding sites…
- PDB
- 3L7Z
- Type
- protein
- Length
- 2,128 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable exosome complex exonuclease 2; Probable exosome complex exonuclease 1; Probable…
- EC
- 3.1.13.-
- UniProt
- Q9UXC0, Q9UXC2, Q9UXC4
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 9 distinct chains · 23% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable exosome complex exonuclease 2 (EC 3.1.13.-) | protein | 251 | 30% helix, 34% strand | Q9UXC0 |
| B | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 232 | 29% helix, 33% strand | Q9UXC2 |
| C | Probable exosome complex RNA-binding protein 1 | protein | 222 | 12% helix, 32% strand | Q9UXC4 |
| D | Probable exosome complex exonuclease 2 (EC 3.1.13.-) | protein | 261 | 28% helix, 32% strand | Q9UXC0 |
| E | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 237 | 28% helix, 32% strand | Q9UXC2 |
| F | Probable exosome complex RNA-binding protein 1 | protein | 215 | 8% helix, 30% strand | Q9UXC4 |
| G | Probable exosome complex exonuclease 2 (EC 3.1.13.-) | protein | 270 | 25% helix, 29% strand | Q9UXC0 |
| H | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 234 | 29% helix, 32% strand | Q9UXC2 |
| I | Probable exosome complex RNA-binding protein 1 | protein | 206 | 10% helix, 32% strand | Q9UXC4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains B, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.79 | 0.85 | 54 | empty |
| 2 | 460 | 0.79 | 0.86 | 61 | empty |
| 3 | 920 | 0.78 | 0.81 | 83 | empty |
| 4 | 628 | 0.77 | 0.83 | 61 | empty |
| 5 | 1002 | 0.73 | 0.76 | 70 | SO4 |
Interfaces
23 interfaces between chains.
- D–E · 2044 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 2008 Ų buried · 45 hydrogen bonds · protein-protein
- G–H · 1969 Ų buried · 48 hydrogen bonds · protein-protein
- B–G · 1363 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1340 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3L7Z · Crystal structure of the S. solfataricus archaeal exosome · the same entry in another collection · chain I against I, TM-score 1.00
- Q9UXC0 · AlphaFold monomer V2.0 prediction for exosome complex component RRP42 (Q9UXC0) · a predicted model of the same protein · chain G 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 Q9UXC0
- Every structure of UniProt Q9UXC2
- Every structure of UniProt Q9UXC4
- Elsewhere: RCSB PDB 3L7Z · PDBe 3L7Z · UniProt Q9UXC0 · UniProt Q9UXC2 · UniProt Q9UXC4
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