MolNFT v1 · #71223 · protein + RNA
Archaeoglobus fulgidus exosome with RNA bound to the active site
3M7N · Putative uncharacterized protein AF_0206: “Archaeoglobus fulgidus exosome with RNA bound to the active site”. X-ray diffraction, 1 ligand (ZN), 19 pockets (best druggability 0.79). MolNFT v1 #71223 on GenesisL1: 3D structure…
- PDB
- 3M7N
- 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
- 19 · best druggability 0.79
Structure
x-ray diffraction · 8 distinct chains · 28% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Putative uncharacterized protein AF_0206 | protein | 179 | 3% helix, 42% strand | O30033 |
| D | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 243 | 33% helix, 36% strand | O29757 |
| E | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 248 | 31% helix, 34% strand | O29757 |
| F | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 246 | 32% helix, 35% strand | O29757 |
| G | Probable exosome complex exonuclease 2 (EC 3.1.13.-) | protein | 254 | 30% helix, 31% strand | O29756 |
| H, I | Probable exosome complex exonuclease 2 (EC 3.1.13.-) | protein | 258 | 31% helix, 31% strand | O29756 |
| X, Y | 5'-R(*C*UP*CP*CP*CP*C)-3' | rna | 5 | — | — |
| Z | 5'-R(*C*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
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.79 | 0.80 | 111 | empty |
| 2 | 880 | 0.78 | 0.81 | 89 | empty |
| 3 | 1001 | 0.76 | 0.78 | 92 | empty |
| 4 | 730 | 0.75 | 0.80 | 75 | empty |
| 5 | 701 | 0.68 | 0.76 | 56 | empty |
Interfaces
27 interfaces between chains.
- F–I · 1530 Ų buried · 33 hydrogen bonds · protein-protein
- E–H · 1516 Ų buried · 26 hydrogen bonds · protein-protein
- D–G · 1497 Ų buried · 29 hydrogen bonds · protein-protein
- D–I · 1394 Ų buried · 22 hydrogen bonds · protein-protein
- F–H · 1369 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3M7N · archaeoglobus fulgidus exosome 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 3M7N · PDBe 3M7N · UniProt O30033 · UniProt O29757 · UniProt O29756
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