Research workbench
The crystal structure of human ARGONAUTE2 bound to a defined guide RNA
Analyse The crystal structure of human ARGONAUTE2 bound to a defined guide RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4W5N
- Type
- protein + RNA
- Length
- 823 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein argonaute-2; RNA (5'- R(P*UP*UP*CP*AP*CP*AP*UP*UP*CP*AP*AP*GP*UP*CP*UP*CP*UP*U)-3'…
- EC
- 3.1.26.-
- UniProt
- Q9UKV8
- Ligands
- IPH, MG
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein argonaute-2 (EC 3.1.26.-) | protein | 806 | 30% helix, 28% strand | Q9UKV8 |
| B | RNA (5'- R(P*UP*UP*CP*AP*CP*AP*UP*UP*CP*AP*AP*GP*UP*CP*UP*CP*UP*U)-3') | rna | 17 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 864 | 0.79 | 0.82 | 85 | IPH, MG |
| 2 | 655 | 0.79 | 0.84 | 74 | empty |
| 3 | 268 | 0.67 | 0.83 | 26 | empty |
| 4 | 232 | 0.59 | 0.80 | 26 | empty |
| 5 | 64 | 0.38 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2383 Ų buried · 61 hydrogen bonds · protein-nucleic
Compared structures
- 4W5N · The Crystal Structure of Human Argonaute2 Bound to a Defined Guide RNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UKV8 · AlphaFold monomer V2.0 prediction for protein argonaute-2 (Q9UKV8) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 4W5N · PDBe 4W5N · UniProt Q9UKV8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.