MolNFT v1 · #41131 · protein
Structure of a 9-subunit archaeal exosome bound to mn ions
2JEB · Exosome complex exonuclease 2: “Structure of a 9-subunit archaeal exosome bound to mn ions”. X-ray diffraction, 2 ligands (MN, CL), 5 pockets (best druggability 0.75). MolNFT v1 #41131 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2JEB
- Type
- protein
- Length
- 703 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exosome complex exonuclease 2; Exosome complex exonuclease 1; Exosome complex RNA-binding…
- EC
- 3.1.13.-
- UniProt
- Q9UXC0, Q9UXC2, Q9UXC4
- Ligands
- MN, CL
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exosome complex exonuclease 2 (EC 3.1.13.-) | protein | 273 | 28% helix, 36% strand | Q9UXC0 |
| B | Exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 233 | 31% helix, 33% strand | Q9UXC2 |
| I | Exosome complex RNA-binding protein 1 | protein | 197 | 16% helix, 34% strand | Q9UXC4 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, I
- CL · Chloride ion · ion · chains B
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.75 | 0.78 | 82 | empty |
| 2 | 446 | 0.61 | 0.76 | 46 | CL |
| 3 | 113 | 0.57 | 0.85 | 21 | empty |
| 4 | 342 | 0.54 | 0.74 | 36 | empty |
| 5 | 92 | 0.33 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1857 Ų buried · 51 hydrogen bonds · protein-protein
- A–I · 313 Ų buried · 1 hydrogen bond · protein-protein
- B–I · 51 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2JEB · Structure of a 9-subunit archaeal exosome bound to Mn ions · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UXC2 · AlphaFold monomer V2.0 prediction for exosome complex component RRP41 (Q9UXC2) · a predicted model of the same protein · chain B against A, TM-score 1.00
- Q9UXC0 · AlphaFold monomer V2.0 prediction for exosome complex component RRP42 (Q9UXC0) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q9UXC4 · AlphaFold monomer V2.0 prediction for exosome complex component RRP4 (Q9UXC4) · a predicted model of the same protein · chain I against A, TM-score 0.84
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 2JEB · PDBe 2JEB · UniProt Q9UXC0 · UniProt Q9UXC2 · UniProt Q9UXC4
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