MolNFT v1 · #36539 · protein + RNA
Crystal structure of aa-ago with externally-bound siRNA
2F8S · 5'-R(P*AP*GP*AP*CP*AP*GP*CP*AP*UP*AP*UP*AP*UP*GP*CP*UP*GP*U…: “Crystal structure of aa-ago with externally-bound siRNA”. X-ray diffraction, 20 pockets (best druggability 0.76). MolNFT v1 #36539 on GenesisL1: 3D structure, binding…
- PDB
- 2F8S
- Type
- protein + RNA
- Length
- 1,452 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(P*AP*GP*AP*CP*AP*GP*CP*AP*UP*AP*UP*AP*UP*GP*CP*UP*GP*U P*CP*UP*UP*U)-3'; Argonaute…
- UniProt
- O67434
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | 5'-R(P*AP*GP*AP*CP*AP*GP*CP*AP*UP*AP*UP*AP*UP*GP*CP*UP*GP*U P*CP*UP*UP*U)-3' | rna | 22 | — | — |
| A, B | Argonaute protein | protein | 704 | 34% helix, 29% strand | O67434 |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.76 | 0.82 | 77 | empty |
| 2 | 513 | 0.74 | 0.83 | 47 | empty |
| 3 | 1062 | 0.74 | 0.77 | 81 | empty |
| 4 | 481 | 0.68 | 0.79 | 57 | empty |
| 5 | 153 | 0.67 | 0.87 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1061 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 929 Ų buried · 100 hydrogen bonds · nucleic-nucleic
- C–A · 464 Ų buried · 6 hydrogen bonds · protein-nucleic
- D–A · 83 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 2F8S · Crystal structure of Aa-Ago with externally-bound siRNA · the same entry in another collection · chain A against A, 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 O67434
- Elsewhere: RCSB PDB 2F8S · PDBe 2F8S · UniProt O67434
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