Research workbench
Archaeoglobus fulgidus exosome Y70A with RNA bound to the active site
Analyse Archaeoglobus fulgidus exosome Y70A with RNA bound to the active site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M85
- Type
- protein + RNA
- Length
- 2,058 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein AF_0206; Probable exosome complex exonuclease 1…
- EC
- 3.1.13.-
- UniProt
- O30033, O29757, O29756
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 7 distinct chains · 28% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Putative uncharacterized protein AF_0206 | protein | 179 | 4% helix, 41% strand | O30033 |
| D | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 243 | 33% helix, 32% strand | O29757 |
| E | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 245 | 32% helix, 34% strand | O29757 |
| F | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 246 | 33% helix, 35% strand | O29757 |
| G, H | Probable exosome complex exonuclease 2 (EC 3.1.13.-) | protein | 258 | 29% helix, 29% strand | O29756 |
| I | Probable exosome complex exonuclease 2 (EC 3.1.13.-) | protein | 259 | 29% helix, 30% strand | O29756 |
| X, Y, Z | 5'-R(*CP*UP*CP*CP*CP*C)-3' | rna | 4 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.79 | 0.81 | 90 | empty |
| 2 | 941 | 0.78 | 0.81 | 84 | empty |
| 3 | 656 | 0.71 | 0.79 | 58 | empty |
| 4 | 264 | 0.71 | 0.85 | 25 | empty |
| 5 | 772 | 0.71 | 0.77 | 82 | empty |
Interfaces
26 interfaces between chains.
- E–H · 1539 Ų buried · 27 hydrogen bonds · protein-protein
- F–I · 1525 Ų buried · 34 hydrogen bonds · protein-protein
- D–G · 1490 Ų buried · 25 hydrogen bonds · protein-protein
- D–I · 1425 Ų buried · 17 hydrogen bonds · protein-protein
- E–G · 1365 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3M85 · Archaeoglobus fulgidus exosome y70a with RNA bound to the active site · the same entry in another collection · chain Z against Z, 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 O30033
- Every structure of UniProt O29757
- Every structure of UniProt O29756
- Elsewhere: RCSB PDB 3M85 · PDBe 3M85 · UniProt O30033 · UniProt O29757 · UniProt O29756
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