Research workbench
Human argonaute-2 bound to a modified siRNA
Analyse Human argonaute-2 bound to a modified siRNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JS2
- Type
- protein + RNA
- Length
- 806 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein argonaute-2; Modified siRNA
- EC
- 3.1.26.-
- UniProt
- Q9UKV8
- Ligands
- IPH, MG, PO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein argonaute-2 (EC 3.1.26.-) | protein | 800 | 32% helix, 28% strand | Q9UKV8 |
| B | Modified siRNA | rna | 6 | — | — |
Ligands and binding sites
- IPH · Phenol · ligand · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.78 | 0.80 | 82 | PO4, MG |
| 2 | 647 | 0.71 | 0.78 | 83 | empty |
| 3 | 101 | 0.47 | 0.80 | 24 | empty |
| 4 | 87 | 0.42 | 0.79 | 21 | empty |
| 5 | 55 | 0.33 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 950 Ų buried · 16 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 6 modified (nucleotide modification).
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 5JS2 · PDBe 5JS2 · UniProt Q9UKV8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.