Research workbench
Human ARGONAUTE2 bound to an siRNA
Analyse Human ARGONAUTE2 bound to an siRNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JS1
- Type
- protein + RNA
- Length
- 811 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein argonaute-2; SiRNA
- EC
- 3.1.26.-
- UniProt
- Q9UKV8
- Ligands
- IPH, MG
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein argonaute-2 (EC 3.1.26.-) | protein | 801 | 32% helix, 29% strand | Q9UKV8 |
| B | SiRNA | rna | 10 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1172 | 0.82 | 0.83 | 87 | MG |
| 2 | 286 | 0.51 | 0.74 | 40 | empty |
| 3 | 104 | 0.45 | 0.79 | 23 | empty |
| 4 | 88 | 0.39 | 0.77 | 24 | empty |
| 5 | 68 | 0.36 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1622 Ų buried · 43 hydrogen bonds · protein-nucleic
Compared structures
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 Q9UKV8
- Elsewhere: RCSB PDB 5JS1 · PDBe 5JS1 · UniProt Q9UKV8
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