Research workbench
Archaeal exosome (RRP4-RRP41(D182A)-RRP42) bound to inorganic phosphate
Analyse Archaeal exosome (RRP4-RRP41(D182A)-RRP42) bound to inorganic phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BA2
- Type
- protein + RNA
- Length
- 725 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable exosome complex exonuclease 2; Probable exosome complex exonuclease 1; Probable…
- UniProt
- Q9UXC0, Q9UXC2, Q9UXC4
- Ligands
- NA, PO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable exosome complex exonuclease 2 | protein | 274 | 27% helix, 36% strand | Q9UXC0 |
| B | Probable exosome complex exonuclease 1 | protein | 234 | 30% helix, 33% strand | Q9UXC2 |
| I | Probable exosome complex RNA-binding protein 1 | protein | 213 | 17% helix, 36% strand | Q9UXC4 |
| R | 5'-R(*AP*AP*AP*AP)-3' | rna | 4 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains B, R, I
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1087 | 0.76 | 0.78 | 83 | empty |
| 2 | 561 | 0.67 | 0.77 | 61 | empty |
| 3 | 395 | 0.62 | 0.77 | 38 | empty |
| 4 | 79 | 0.47 | 0.82 | 13 | empty |
| 5 | 135 | 0.41 | 0.74 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1900 Ų buried · 45 hydrogen bonds · protein-protein
- B–R · 422 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–I · 348 Ų buried · 1 hydrogen bond · protein-protein
- A–R · 320 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–I · 50 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4BA2 · Archaeal exosome (Rrp4-Rrp41(D182A)-Rrp42) bound to inorganic phosphate · 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 0.99
- 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 0.99
- 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 0.86
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 4BA2 · PDBe 4BA2 · UniProt Q9UXC0 · UniProt Q9UXC2 · UniProt Q9UXC4
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